US5589579A - Gene sequence and probe for a marker of non-small cell lung carinoma - Google Patents

Gene sequence and probe for a marker of non-small cell lung carinoma Download PDF

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US5589579A
US5589579A US08/276,919 US27691994A US5589579A US 5589579 A US5589579 A US 5589579A US 27691994 A US27691994 A US 27691994A US 5589579 A US5589579 A US 5589579A
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seq
protein
lung cancer
hcaviii
gene
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Richard M. Torczynski
Arthur P. Bollon
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Exegenics Inc
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Cytoclonal Pharmaceutics Inc
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Assigned to CYTOCLONAL PHARMACEUTICS, INC. reassignment CYTOCLONAL PHARMACEUTICS, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BOLLON, ARTHUR P., TORCZYNSKI, RICHARD M.
Priority to CA002195403A priority patent/CA2195403A1/en
Priority to PCT/US1995/009145 priority patent/WO1996002552A1/en
Priority to US08/776,088 priority patent/US5773579A/en
Priority to JP8505257A priority patent/JPH10503087A/en
Priority to AU33592/95A priority patent/AU700915B2/en
Priority to EP95930093A priority patent/EP0804451A4/en
Priority to BR9508417A priority patent/BR9508417A/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/88—Lyases (4.)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Definitions

  • the invention relates to genes and proteins specific for certain cancers and methods for their detection.
  • Lung cancer is the most common form of cancer in the world. Estimates for the year 1985 indicate that there were about 900,000 cases of lung cancer worldwide. (Parkin, et el., "Estimates of the worldwide incidence of eighteen major cancers in 1985," Int J Cancer 1993; 54:594-606). For the United States alone, 1993 projections placed the number of new lung cancer cases at 170,000, with a mortality of about 88%. (Boring, et al., "Cancer statistics," CA Cancer J Clin 1993; 43:7-26). Although the occurrence of breast cancer is slightly more common in the United States, lung cancer is second behind prostate cancer for males and third behind breast and colorectal cancers for women. Yet, lung cancer is the most common cause of cancer deaths.
  • the World Health Organization classifies lung cancer into four major histological types: (1) squamous cell carcinoma (SCC), (2) adenocarcinoma, (3) large cell carcinoma, and (4) small cell lung carcinoma (SCLC).
  • SCC squamous cell carcinoma
  • SCLC small cell lung carcinoma
  • MAbs for lung cancer were first developed to distinguish NSCLC from SCLC.
  • Mulshine, et al. "Monoclonal antibodies that distinguish nonsmall-cell from small-cell lung cancer,” J Immunol 1983; 121:497-502).
  • the identity of the cell surface antigen with which a particular antibody reacts is not known, or has not been well characterized.
  • Scott, et al. "Early lung cancer detection using monoclonal antibodies," In: Lung Cancer. Edited by J. A. Roth, J. D. Cox, and W. K. Hong. Boston: Blackwell Scientific Publications, 1993:310-324).
  • Carcinoembryonic antigen is a frequently studied tumor marker of cancer including lung cancer.
  • Squamous cell carcinoma antigen is another established serum marker.
  • Margolis, et al. "Serum tumor markers in non-small cell lung cancer,” Cancer 1994; 73:605-609 - ).
  • serum antigens for lung cancer include antigens recognized by MAbs 5E8, 5C7, and 1F10, the combination of which distinguishes between patients with lung cancer from those without (Schepart, et al., "Monoclonal antibody-mediated detection of lung cancer antigens in serum,” Am Rev Respir Dis 1988; 138:1434-8), Furthermore, the combination of 5E8, 5C7 and 1F10 was more sensitive, specific and accurate for identifying NSCLC when compared to results from a combination of the CEA and squamous cell carcinoma antigen tests. (Margolis, et al., Cancer 1994; 73:605-609).
  • Serum CA 125 Serum CA 125, initially described as an ovarian cancer-associated antigen, has been investigated for its use as a prognostic factor in NSCLC.
  • Diez, et al. "Prognostic significance of serum CA 125 antigen assay in patients with non-small cell lung cancer," Cancer 1994; 73:1369-76).
  • MAbs may not be the answer to early detection because there has only been moderate success with immunologic reagents for paraffin-embedded tissue.
  • lung cancer may express features that cannot be differentiated by antibodies; for example, chromosomal deletions, gene amplification, or translocation and alteration in enzymatic activity.
  • cytogenetic and molecular techniques may provide powerful tools for screening, diagnosis, management and ultimately treatment of lung cancer.
  • An example of a lung cancer antigen that has been cloned is the adenocarcinoma-associated antigen.
  • This antigen, recognized by KS1/4 MAb is an epithelial malignancy/epithelial tissue glycoprotein from the human lung adenocarcinoma cell line UCLA-P3. (Strnad, et al., "Molecular cloning and characterization of a human adenocarcinoma/epithelial cell surface antigen complementary DNA," Cancer Res 1989; 49:314-317).
  • the antigen has been found on all adenocarcinoma cells tested and in various corresponding normal epithelial cells.
  • Northern blot analysis indicated that transcription of the adenocarcinoma-associated antigen was detected in RNA isolated from normal colon but not in RNA isolated from normal lung, prostate, or liver. Therefore identification of adenocarcinoma-associated antigen in lung cells may prove to be diagnostic for adenocarcinoma.
  • NCA nonspecific crossreacting antigen
  • lung cancer cells fall into three different types according to their CEA and/or NCA expression by Northern blot analysis. Specifically, lung cancers expressed both CEA and NCAmRNA, only NCAmRNA, or neither mRNA. CEA-relatedmRNA expression was always accompanied by NCAmRNA expression and there were no cases of CEAmRNA expression alone.
  • the separate assessment of CEA and NCA expression in lung cancers may be important in determining the prognosis of lung cancers because the antigens have been described as cell-cell adhesion molecules and may play a role in cancer metastasis.
  • In situ hybridization uses nucleic acid probes that recognize either repetitive sequences on a chromosome or sequences along the whole chromosome length or chromosome segments. By tagging the probes with radioisotopes or color detection systems, chromosome regions can be identified within the cell. Investigations using in situ hybridization have demonstrated numerous chromosomal abnormalities in samples from human tumors, including bladder, neuroectodermal, breast, gastric and lung cancer tumors. (Kim, et al., "Interphase cytogenetics in paraffin sections of lung tumors by non-isotopic in situ hybridization. Mapping Genotype/phenotype heterogeneity," Am J Pathol 1993; 142:307-317).
  • Fluorescent in situ hybridization allows cells to be stained so that genetic aberrations resulting in changes in gene copy number or structure can be quantitated by fluorescent microscopy.
  • a chemically labeled single-stranded nucleic acid probe homologous to the target nucleic acid sequence is annealed to denatured nucleic acid contained in target cells.
  • the cells may be mounted on a microscope slide, in suspension or prepared from paraffin-embedded material. Treating the chemically modified probes with a fluorescent ligand makes the bound probe visible.
  • FISH has been used for (1) detection of changes in gene copy number and gene structure; (2) detection of genetic changes, even in low frequency subpopulations; and (3) detection and measurement of the frequency of residual malignant cells.
  • oncogenes are activated by mutation and lead to deregulated cellular growth.
  • genes code for proteins that function as growth factors, growth factor receptors, signal transducing proteins and nuclear proteins involved in transcriptional regulation. Amplification, mutation, and translocations have been documented in many different cancer cells and have been shown to lead to gene activation or overexpression.
  • the ras family of oncogenes comprises a group of membrane associated GTP-binding proteins thought to be involved in signal transduction. Mutations within the ras oncogenes, resulting in sustained growth stimulation, have been identified in 15 to 30% of human NSCLC. (Birrer, et al., "Application of molecular genetics to the early diagnosis and screening of lung cancer," Cancer 1992; 52suppl; 2658s-2664s). Patients with tumors containing ras mutations had decreased survival compared with patients whose tumors had no ras mutations.
  • PCR Polymerase chain reaction
  • erb B family Another family of dominant oncogenes, the erb B family, has been found to be abnormally expressed in lung cancer cells. This group codes for membrane-associated tyrosine kinase proteins and contains erb B1, the gene coding for the epidermal growth factor (EGF) receptor, and erb B2 (also called Her-2/neu).
  • EGF epidermal growth factor
  • erb B1 also called Her-2/neu
  • the erb B1 gene has been found to be amplified in NSCLC (up to 20% of squamous cell tumors), while the EGF receptor has been shown to be overexpressed in many NSCLC cells (approximately 90% of squamous cell tumors, 20 to 75% of adenocarcinomas, and rarely in large cell or undifferentiated tumors).
  • a third family of dominant oncogenes involved in lung cancer is the myc family. These genes encode nuclear phosphoproteins, which have potent effects on cell growth and which function as transcriptional regulators. Unlike ras genes, which are activated by point mutations in lung cancer cells, the myc genes are activated by overexpression of the cellular myc genes, either by gene amplification or by rearrangements, each ultimately leading to increased levels of myc protein. Amplification of the normal myc genes is seen frequently in SCLC and rarely in NSCLC.
  • Tumor suppressor genes function normally to suppress cellular proliferation, and since they are recessive oncogenes, mutations or deletions must occur in both alleles of these genes before transformation occurs.
  • a phosphoprotein p53 which is encoded by a gene located on chromosome 17p, suppresses transformation in its wild-type state. While in its mutant state, p53 acts as a dominant oncogene. p53 functions in DNA binding and transcription activation. Mutations of p53 have been found in many human cancers including colon, breast, brain and lung cancer cells. (Birrer, et al., Cancer Res.(suppl) 1992, 52:2658s-2664s). In NSCLC cell lines, p53 mutations have been found at a rate of up to 74%. (Mitsudomi, et al., "p53 gene mutations in non-small-cell lung cancer cell lines and their correlation with the presence of ras mutations and clinical features," Oncogene 1992; 7:171-180).
  • a lung cancer marker antigen specific for NSCLC, has now been found, sequenced, and cloned.
  • the antigen is useful in methods for detection of non-small cell lung cancer and for potential production of antibodies and probes for treatment compositions.
  • FIGURE 1 depicts the alignment of the amino acid sequence of HCAVIII with Previously described carbonic anhydrases. conserveed amino acids are shown in bold.
  • the invention concerns a lung cancer antigert (HCAVIII) gene specific for non-small cell lung cancer.
  • the invention relates to an isolated substantially purified nucleic acid encoding the protein sequence shown in SEQ ID NO:2, and may be mRNA.
  • the invention relates to cDNAs which encode a protein having a signal sequence (SEQ ID NO:2), or the mature form of the protein (SEQ ID NO:4), or a truncated form of the protein lacking the transmembrane domain (SEQ ID NO:10), or a protein in which one or more amino acids in the phosphorylation region of the protein have been altered to affect that function, an example of which is shown in SEQ ID NO:13.
  • proteins encoded by the cDNA of SEQ ID NO:1, or SEQ ID NO:3 or SEQ ID NO:9, or a cDNA altered in the phosphorylation region, an example of which is SEQ ID NO:12, are provided.
  • the invention relates to a transcribable recombinant DNA clone for HCAVIII.
  • expression vectors for HCAVIII and modifications thereof are an object.
  • the invention further relates to methods of detection of lung cancer.
  • an in situ hybridization technique is provided.
  • a fluorescence in situ hybridization technique is provided.
  • an ELISA assay is provided.
  • detection of carbonic anhydrase activity which correlates with lung cancer antigen is provided.
  • HCAVIII cell surface protein
  • the HCAVIII cDNA in the vector pLC56 has been sequenced and characterized including the entire coding region and substantially all of the upstream and downstream non-translated regions.
  • the cDNA in pLC56 was sequenced on both strands from exonuclease III-generated deletions and subsequent subcloning into M13 vectors or directly from the cloning vectors using the di-deoxy method and a SEQUENASE ® Version 2.0 kit (U.S. Biochemicals, Cleveland, Ohio). Additional regions of DNA were subcloned as small restriction fragments into the same vectors for sequence analysis. Overlapping segments were ordered using MacVector Align software (Kodak/IBI Technologies, New Haven Conn.).
  • SEQ ID NO:1 represents the cDNA encoding HCAVIII and a presumed signal peptide.
  • SEQ ID NO:2 represents the signal peptide (amino acid residues -29 to -1) followed by the mature protein (amino acid residues 1 to 325).
  • a protein of about 354 amino acids is encoded with the predictive size of 39448 daltons.
  • a hydrophilicity plot (MacVector software, Kodak/IBI Technologies) of this protein provided strong evidence of a leader peptide at the N-terminus and a membrane-spanning segment near the C-terminus.
  • the membrane-spanning segment provides evidence that this protein is membrane bound, as also predicted by its positive selection with panning methodology (See Watson, et al., Recombinant DNA, 2nd ed., pp. 115-116, 1992).
  • the cleavage site of the signal as predicted by yon Heijne is 29 amino acids down from the N-terminus methionine.
  • SEQ ID NO:3 corresponds approximately to the coding region of the mature polypeptide.
  • the subsequent "mature" protein is proposed to be 325 amino acids, initiating with serine, and of a calculated 36401 daltons and a pI of 6.42 (SEQ ID NO:4).
  • This protein is identified as a carbonic anhydrase (CA) based on the conservation of amino acids at positions critical for the binding of Zn +2 , critical for the catalysis of CO 2 , as well as numerous other conserved amino acids (see FIG. 1).
  • CA carbonic anhydrase
  • the protein is 34 to 64 amino acids longer (at the C-terminus) than any previously reported carbonic anhydrase by virtue of the membrane-spanning region, also found in HCAIV and an additional approximate 30 amino acids on the cytoplasmic side of the cell, which are apparently missing in other human CA isoforms.
  • this intracellular domain contains a phosphorylation site recognized by protein kinase C and other kinases, as defined by the motif "Arg--Arg--Lys--Ser” (SEQ ID NO:5 and SEQ ID NO:6) (amino acid residues 1-4 in SEQ ID NO:6 and amino acid residues 299-302 in SEQ ID NO:2 and SEQ ID NO:4).
  • this motif is found only in HCAVIII, and at a functionally significant site, i.e., within the cytosol. A surface cleft essential for enzymatic function present on other carbonic anhydrases is conserved for this protein, suggesting this protein will confer enzymatic activity.
  • HCAVI has been isolated from sheep salivary glands in a dimer conformation, by virtue of intermolecular disulfide bonds derived from cysteines at positions conserved in sheep and human HCAVI as well as the protein encoded by pLC56, but not other human CA's. Consequently, HCAVIII is likely presented on the cell surface as a dimer of a predicted 72804 daltons.
  • five possible N-glycosylation sites are predicted by the primary amino acid sequence and the motif "Asn--Xaa--Ser (Thr)", beginning at amino acid residues -2, 51, 133, 151, and 202 in SEQ ID NO:2, respectively.
  • HCAVIII is expressed at a much higher level in a non-small cell lung cancer cell line (A549) than in normal lung tissue, other normal tissues, and other tumor cell lines which makes it useful in distinguishing this disease. This is clearly demonstrated in Table 1. Data for this table was obtained as follows. Total cellular RNA was isolated from the indicated actively growing cell lines as described by Chirgwin, et al., "Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease," Biochemistry 1979; 18:5294-5299. RNA samples were fractionated over a 1% agarose-formaldehyde gel and transferred to a nylon membrane (Qiagen, Chatsworth, Calif.) by capillary action.
  • the hybridization probe was generated from a 1 kilobase pair BstXI restriction fragment isolated from pLC56, a plasmid harboring the HCAVIII gene in its initial isolation. This fragment was radiolabeled with 32 p using a PRIME-IT® Random Primer Labeling Kit obtained from Stratagene, La Jolla, Calif. A membrane containing RNA derived from healthy human tissue was purchased from Clonetech Laboratories, Inc., Palo Alto, Calif. RNA blots were hybridized in a standard cocktail containing 32 P-labeled probe at 42° C. overnight then exposed to X-ray film. The same blots were subsequently, upon removal of the probe, rehybridized with a second 32 P-labeled DNA from ⁇ -actin to serve as a positive control for integrity of the blotted RNA.
  • probes are made corresponding to sequences of the cDNA shown in SEQ ID NO:3, which are complimentary to the mRNA for HCAVIII.
  • These probes can be radioactively or non-radioactively labeled in a number of ways well known to the art.
  • the probes can be made of various lengths. Such factors as stringency and GC content may influence the desired probe length for particular applications.
  • the probes correspond to a length of 10-986 nucleotides from SEQ ID NO:3.
  • the labeled probes can then be bound to detect the presence or lack of mRNA encoding HCAVIII in biopsy material through in situ hybridization.
  • the mRNA is expected to be associated with the presence of non-small cell tumors and to be a marker for the precancerous condition as well.
  • In situ hybridization provides a specificity to the target tissue that is not obtainable in Northern, PCR or other probe-driven technologies. In situ hybridization permits localization of signal in mixed-tissue specimens commonly found in most tumors and is compatible with many histologic staining procedures.
  • This technique is comprised of three basic components: first is the preparation of the tissue sample provided by the pathologist to permit successful hybridization to the probe. Second is the preparation of the hybridization probe, typically a RNA complementary to the mRNA of the gene of interest (i.e., antisense RNA).
  • RNA probes are preferred over DNA probes for in situ hybridizations mainly because background hybridization of the probe to irrelevant nucleic acids or nonspecific attachment to cell debris or subcellular organelles can be eliminated with RNAse treatment post-hybridization.
  • Third is the hybridization and method of detection post-hybridization.
  • the RNA transcript probe has been radiolabeled by the incorporation of 32 p or 35 S nucleotides to permit subsequent detection of the probed specimen by autoradiography or quantitation of silver grains following treatment with autoradiographic emulsion. Nonradioactive detection systems have also been developed.
  • biotinylated nucleotides can be substituted for the radioactive nucleotide in the RNA probe preparation, permitting visualization of the probed sample by immunocytochemistry-derived techniques.
  • Example 1 describes in situ hybridization procedures using RNA probes derived from the HCAVIII gene, and
  • Example 2 provides exemplary fluorescent in situ (FISH) hybridization procedures.
  • the cDNA for HCAVIII (SEQ ID NO:3) is currently in an expression vector which is be used to generate the protein in E. coli.
  • This expression system described in Example 3 produces HCAVIII to be used as an antigen for the generation of antibodies (Example 4) for use in an ELISA assay to detect shed HCAVIII in body fluids as described in Example 5.
  • the methods for production of antibodies and ELISA type assays are well known in the art. Exemplary methods and components of these procedures have been chosen and developed and are described in Examples 4 and 5.
  • E. coli The expression and purification of foreign proteins in E. coli is often problematic. On occasion, the protein is expressed at high levels but is deposited within the cell as an insoluble, denatured form termed an inclusion body. These bodies are often observed when the foreign protein contains a hydrophobic domain, such as found in the membrane spanning segment of HCAVIII.
  • the DNA sequences encoding the membrane spanning segment of HCAVIII are deleted.
  • the protein expressed in E. coli from this engineered plasmid is now in a soluble and native form within the cell, permitting a rapid and less harsh purification.
  • the ELISA test to measure HCAVIII shed into body fluids as described in Example 5 relies on the recombinant protein produced from E. coli.
  • the shed antigen is a membrane-bound receptor that has been released from the membrane spanning segment anchoring it to the cell. Consequently, the recombinant HCAVIII engineered to remove the membrane spanning segment is a more accurate representation of the putative HCAVIII shed antigen found in specimens and may prove to be the preferred antigen for polyclonal antisera and monoclonal antibody production as described for the development of an ELISA test.
  • a first plasmid is constructed by cleaving pLC56 with the restriction enzyme Tth111 I, followed by treatment with T 4 -DNA polymerase and dGTP, and finally with alkaline phosphatase to remove 5'-terminal phosphates.
  • the DNA sample is then purified by phenol/chloroform extraction and ethanol precipitation.
  • the sample is digested with the restriction endonuclease BspE1, then the fragments are resolved by agarose gel electrophoresis to permit the isolation of a 267 base pair fragment.
  • a second plasmid described previously for expression of the HCAVIII mature protein (SEQ ID NO:4), is cleaved with EcoRI and BspE1 followed by alkaline phosphatase treatment and purification by phenol/chloroform extraction and ethanol precipitation.
  • oligonucleotides are synthesized, being 5'-TGAGTCGACG (SEQ ID NO:7) and 5'-AATTCGTCGACTCA (SEQ ID NO:8), that complement each other and upon annealing, provide a termination codon (TGA) and sequence complementary to EcoRI cleaved DNA.
  • TGA termination codon
  • the two oligonucleotides, the 267 base pair fragment, and the BspEI/EcoRI cleaved plasmid will be combined in a ligation reaction, and the resultant plasmid which contains the truncated DNA sequence (SEQ ID NO:9) are used to transform competent E. coli.
  • the resulting truncated protein (SEQ ID NO:10) is 271 amino acids and of a size consistent with other HCA's but lacking the membrane spanning segment and the intracellular domain.
  • An exemplary plasmid is produced in which the "Ser” codon (amino acid residue 4 of SEQ ID NO:6; amino acid residue 302 in SEQ ID NO:2 and SEQ ID NO:4), is converted to a "Gly” codon using an in vitro mutagenesis technique described in Example 3 and previously recited in Kunkel, Thomas, "Rapid and efficient site-specific mutagenesis without phenotypic selection," Proc Natl Acad Sci USA 1985; 82:488-492, and the oligonucleotide 5'-CTTTTTTGATACCCTTCCTTCTGAA (SEQ ID NO:11) (located in SEQ ID NO:1 at the base pairs 1010-1034 with 1022 as the mutagenized base pair).
  • the DNA sequences containing the HCAVIII gene engineered for production of the mature protein and mutagenized codon is released from the mutagenesis vector by BamHI and EcoRI restriction endonucleases and ligated into pGEX4T1 cleaved with the same enzymes, and the resultant plasmid is used to transform competent E. coli.
  • the codon mutagenesis is confirmed by DNA sequence analysis, and the protein is expressed and purified from E. coli as described in Example 3.
  • the DNA sequence of the altered plasmid as shown in SEQ ID NO:12 differs from the gene encoding the mature protein (SEQ ID NO:2) in that the nucleotide 1022 (nucleotide 904 in SEQ ID NO:12) is changed from “A” to "G” and the protein sequence (SEQ ID NO:13) expressed by the altered plasmid is identical to the mature protein (SEQ ID NO:4) except that amino acid residue 302 is changed from "Ser" to "Gly.”
  • HCAVIII Another way to detect the presence of increased HCAVIII could be to assay for levels of carbonic anhydrase activity in biopsy materials as described in Example 6. This should be a useful test as HCAVIII, although it is an immunologically unique molecule, contains small but distinct regions which are conserved between previously reported carbonic anhydrase proteins.
  • primers are made complimentary to the HCAVIII cDNA (SEQ ID NO:3) for detecting expression of the gene. PCR amplification of cDNA from lung biopsy cells would indicate the presence of the same non-small cell lung carcinoma.
  • HCAVIII Due to the non-small cell lung cancer specificity of HCAVIII and the gene encoding the protein, antibodies specific for HCAVIII would also exhibit non-small cell lung cancer specificity which can be employed for diagnostic detection of HCAVIII in body fluids such as serum or urine or HCAVIII containing cells. Targeting of cancer therapeutic drugs to HCAVIII containing cells can also be developed using HCAVIII specific antibodies.
  • the genetic expression of the gene encoding HCAVIII could be modulated by drugs or anti-sense technology resulting in an alteration of the cancer state of the HCAVIII containing cells.
  • Tissue samples are treated with 4% paraformaldehyde (or an equivalent fixative), dehydrated in sequential ethanol solutions of increasing concentrations (e.g., 70%, 95% and 100%) with a final xylene incubation (see Current Protocols in Molecular Biology, pp. 14.01-14.3 and Immunocytochemistry II:IBRO Handbook Series: Methods in the Neurosciences Vol 14; pp 281-300, incorporated herein by reference).
  • the tissue is embedded in molten paraffin, molded in a casting block and can be stored at room temperature.
  • Tissue slices typically 8 ⁇ m thick, are prepared with a microtome, dried onto gelatin-treated glass slides and stored at -20° C.
  • DNA sequences from the HCAVIII gene are subcloned into a plasmid engineered for production of RNA probes.
  • a 776 bp DNA fragment is released from a pLC56 plasmid following BamHI/AccI digestion, where the BamHI site has been created by in vitro mutagenesis (see E. coli expression below).
  • This fragment is ligated into pGEM-2 (Promega Biotec, Madison, Wis.) that was cleaved with BamHI and AccI and transformed into competent E. coli.
  • This constructed plasmid contains the T7 RNA polymerase promoter downstream of the AccI restriction site and hence can drive transcription of the antisense HCAVIII sequences defined by the BamHI/AccI fragment.
  • an in vitro transcription reaction composed of transcription buffer (40 mM Tris-HCl, pH 7.5, 6 mMMgCl 2 , 2 mM spermidine, 10 mM NaCl, 10 mM dithiothreitol, 1 u/ul ribonuclease inhibitor), linearized plasmid, 10 mM GTP, 10 mM ATP, 10 mM CTP, 100 ⁇ Ci of ( 35 S)UTP, and T7 RNA polymerase is incubated at 37° C.
  • transcription buffer 40 mM Tris-HCl, pH 7.5, 6 mMMgCl 2 , 2 mM spermidine, 10 mM NaCl, 10 mM dithiothreitol, 1 u/
  • RNA copies of the gene are produced that are used as a hybridization probe.
  • the reaction is terminated by the addition of DNase, and the synthesized RNA is recovered from unincorporated nucleotides by phenol/chloroform extraction and sequential ethanol precipitations in the presence of 2.5M ammonium acetate.
  • the slides containing fixed, sectioned tissues are rehydrated in decreasing concentrations of ethanol (100%, 70% and 50%), followed by sequential treatments with 0.2N HCl, 2X SSC (where 20X SSC is 3M NaCl and 0.3M sodium citrate) at 70° C. to deparaffinate the sample, phosphate buffered saline (PBS), fixation in 4% paraformaldehyde and PBS wash.
  • PBS phosphate buffered saline
  • fixation in 4% paraformaldehyde and PBS wash The slides are blocked to prevent nonspecific binding by the sequential additions of PBS/10 mM dithiothreitol (45° C.), 10 mM dithiothreitol/0.19% iodoacetamide/0.12% N-ethylmaleimide and PBS wash.
  • the slides are equilibrated in 0.1M triethylamine, pH 8.0, followed by treatment in 0.1M triethylamine/0.25% acetic anhydride and 0.1M triethylamine/0.5% acetic anhydride and washed in 2X SSC.
  • the slides are then dehydrated in increasing concentrations of ethanol (50%, 70% and 100%) and stored at -80° C.
  • a hybridization mix is prepared by combining 50% deionized formamide, 0.3M NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1X Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, 0.02% bovine serum albumin (BSA)), 500 ⁇ g/ml yeast tRNA, 500 ⁇ g/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000 and the 35 S-labeled RNA probe. This solution is placed on the fixed, blocked tissue slides which are then incubated at 45° C. in a moist chamber for 0.5 to 3 hours.
  • the slides are washed to remove unbound probe in 50% formamide, 2X SSC, 20 mM 2-mercaptoethanol (55° C.), followed by 50% formamide, 2X SSC, 20 mM 2-mercaptoethanol and 0.5% Triton-X 100 (50° C.) and finally in 2X SSC/20 mM 2-mercaptoethanol (room temperature).
  • the slides are treated with 10 mM Tris-HCl, pH 8.0/0.3M NaCl/40 ⁇ g/ml RNase A/2 ⁇ g/ml RNAse T1 (37° C.) to reduce levels of unbound RNA probe.
  • the slides are washed in formamide/SSC buffers at 50° C., and room temperature and then dehydrated in increasing ethanol concentrations containing 0.3M ammonium acetate, and one final 100% ethanol wash.
  • the slides are then exposed to X-ray film followed by emulsion autoradiography to detect silver grains.
  • Test tissue samples are compared to matched controls derived from normal lung tissue.
  • Evidence of elevated transcription of the HCAVIII genes in test tissue compared to normal tissue, as determined by autoradiography (X-ray film) or alternatively by the quantitation of silver grains following emulsion autoradiography would provide evidence of a positive diagnosis for lung cancer.
  • FISH Fluorescent In situ Hybridization
  • a genomic clone to the HCAVIII genes (SEQ ID NO:1) is isolated using a PCR primer pair which have been identified from the pLC56 cDNA sequence. This primer pair is located in putative exon 6 of the pLC56 genes, and they are identified as Probe Exon 6A (5'-ACATTGAAGAGCTGCTTCCGG-3'; SEQ ID NO:14) and Probe Exon 6B (5'-AATTTGCACGGGGTTTCGG-3'; SEQ ID NO:15).
  • the genomic clone of HCAVIII is then identified as a PCR product of about 119 bp using this primer pair from the designated genomic clone. This result is confirmed by Southern blotting and DNA sequence analysis.
  • the DNA probe comprising the genomic clone of HCAVIII plus flanking sequences is labeled in a random primer reaction with digoxigenin-11-dUTP (Boehringer Mannheim Biochemicals, Indianapolis, Ind.) by combining the DNA with dNTP(-TTP, final 0.05 mM), digoxigenin-11-dUTP/dTTP (0.0125 mM and 0.0375 mM, final), 10 mM 2-mercaptoethanol, 50 mM Tris-HCl, pH 7.5, 10 mMMgCl 2 , 20 U of DNA polymerase I and 1 ng/ml DNase. The reaction is incubated at 15° C.
  • a hybridization mix is prepared by combining 50% deionized formamide, 0.3M NaCl, 10 mMTris-HCl, pH 8.0, 1 mM EDTA, 1X Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, and 0.02% bovine serum albumin), 500 ⁇ g/ml yeast tRNA, 500 ⁇ g/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000, and the labeled DNA probe.
  • the slides are washed three times with a solution comprising 50% formamide and 2X SSC at 42° C., washed twice in 2X SSC at 42° C., and finally washed in 4X SSC at room temperature.
  • the slide is blocked with a solution of 4X SSC and 1% BSA, and then washed with a solution of 4X SSC and 1% Triton X-100.
  • the hybridized digoxigenin-labeled probe is detected by adding a mixture of sheep anti-digoxigenin antibody (Boehringer Mannheim) diluted in 0.1M sodium phosphate, pH 8.0, 5% nonfat dry milk, and 0.02% sodium azide, followed by the addition of fluorescein-conjugated rabbit anti-sheep IG for detection.
  • the slides are then washed in PBS, mounted in Vectashield (Vector Laboratories, Inc., Burlingame, Calif.), and viewed by fluorescent microscopy.
  • Hybridization signals are enumerated in tumor derived tissue and then compared to normal tissue. Normal tissue displays two distinct hybridization signal characteristics of a diploid state. Enumeration over the rate of two hybridization signals/cell is considered significant.
  • E. coli expression is often performed in E. coli when an immunogen or large amounts of protein are desired, as in the development of a diagnostic kit.
  • a preferred system for E. coli expression has been described (Smith, et al., "Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione-s-transferase," Gene 1988; 67:31-40) whereby glutathione transferase is expressed with amino acids representing the cloned protein of interest attached to the carboxylterminus.
  • the fusion protein can then be purified via affinity chromatography and the protein of interest fused to glutathione transferase released by digestion with the protease thrombin or alternatively the fusion protein is released intact from the affinity column by competing levels of free glutathione.
  • HCAVIII protein SEQ ID NO:4 of this invention in E. coli using the above described technology
  • an expression plasmid was produced in which the glutathione transferase gene was fused in frame with the HCAVIII gene (SEQ ID NO:1) to produce a fusion protein.
  • the fusion gene/expression plasmid was assembled from nucleic acids derived from the following sources.
  • the expression plasmid pGEX4T1 (Pharmacia, Piscataway, N.J.) was cleaved in the polycloning region with the restriction endonucleases BamHI and EcoRI to permit insertion of the HCAVIII gene.
  • an oligonucleotide was synthesized, being 5'-GTCCACTTGGATCCGTTCACTGG-3' (SEQ ID NO:16).
  • Kunkel Proc Natl Acad Sci USA 1985; 82:488-492
  • a BamHI restriction site was created without altering the amino acid codons of the original protein.
  • the created BamHI site was situated in correct reading frame and proximity to the predicted cleavage site separating the signal peptide from the mature protein.
  • the DNA sequences encoding the mature protein were released from the mutagenesis vector as a BamHI/EcoRI fragment, where the EcoRI site originates from a polycloning region of the DNA sequencing vector pUC19 found downstream of the HCAVIII gene.
  • the DNA fragments described above comprised of pGEX4T-1 cleaved at BamHI and EcoRI and the HCAVIII gene released as a BamHI/EcoRI fragment were combined in a mixture composed of 1X T 4 ligase buffer (50 mM Tris-HCl, 10 mMMgCl 2 , 20 mM dithiothreitol, 1 mMATP, 50 ⁇ g/ml BSA, final pH 7.5) and T 4 DNA ligase (New England Biolabs, Beverly, Mass.).
  • the ligated DNA was used to transform a suitable strain of E. coli such as XL-1 Blue (Stratagene).
  • the recovered plasmid is sequenced to confirm the expected DNA sequence.
  • Protein expression is induced in E. coli with the chemical isopropyl ⁇ -thiogalactoside, and the fusion protein is released by cell lysis, binding to an affinity column composed of glutathione-agarose (Sigma, St. Louis, Mo.) and cleavage with thrombin to release the HCAVIII protein.
  • the resulting protein is suitable as an immunogen for polyclonal or monoclonal antibody production and for usage in an ELISA kit as an internal standard and positive control.
  • the length of the resulting protein can be varied by altering the length of SEQ ID NO:1 prior to insertion into the expression plasmid, or by cleavage of amino acids from the protein resulting in the above example.
  • Structure/function studies of other HCA's suggest modifications (as defined by deletions at the N-terminal and C-terminal) more extensive than disclosed in SEQ ID NO:9 would still permit the production and use of a protein as an immunogen or standard, these deletions being a protein defined by about amino acid residue 3 to amino acid residue 259 in SEQ ID NO:9.
  • Using existing technology one could synthesize a peptide of approximately 10 to 40 amino acids in length that comprises a structural domain of HCAVIII. This synthesized peptide, coupled to a carrier protein, could be used for generating polyclonal antisera specific for native HCAVIII.
  • mice are immunized with either the purified HCAVIII protein or a glutathione/HCAVIII fusion protein. Following cell fusion, selection for hybrid cells' and subcloning, hybridomas are screened for a positive antibody against whole A549 cells or purified HCAVIII protein using an indirect ELISA assay as described for the ELISA kit (see Example 5).
  • An indirect ELISA screening assay for HCAVIII protein (SEQ ID NO:4) has been designed to detect and monitor the HCAVIII protein in body fluids including but not limited to serum and other biological fluids such as sputum or bronchial effluxion at effective levels necessary for sensitive but accurate determinations. It is intended to aid in the early diagnosis of non-small cell cancer, for which there currently is no effective treatment. An early-detection, accurate, non-invasive assay for non-small cell lung cancer would be of great benefit in the management of this disease.
  • the immunochemicals used in this procedure are rabbit anti-human HCAVIII antibody (purified IgG, IgM) which is produced according to the procedure given in Example 4, mouse anti-human HCAVIII (monoclonal) also produced according to the procedure given in Example 4, and goat anti-Rabbit IgG/peroxidase conjugate.
  • the HCAVIII protein standard and internal positive control are produced as described in Example 3 for expression in E. coli.
  • Substrate components include 2M H 2 SO 4 stored at room temperature; dimethylsulfoxide (Sigma Chemical Co., St. Louis, Mo.) stored at room temperature in a tightly capped bottle; 3',5,5'-tetramethylbenzidine (TMB) (Sigma Chemical Co.) used as a peroxidase substrate and stored at room temperature in the dark to prevent exposure to light; and hydrogen peroxide, 30%.
  • TMB 3',5,5'-tetramethylbenzidine
  • Phosphate buffered saline is prepared by adding 32.0 g sodium chloride, 0.8 g potassium phosphate, monobasic, 0.8 g potassium chloride, and 4.6 g sodium phosphate, dibasic, anhydrous, to 3.2 L deionized water and mixing to dissolve. After bringing the solution to 4 L with deionized water and mixing, the pH is adjusted to about 7.2. The buffer is stored at 4° C. for a maximum of 3 weeks.
  • the carbonate/bicarbonate coating buffer is prepared by mixing 1.45 g sodium carbonate and 7.25 g sodium bicarbonate in 800 ml deionized water until dissolved. The solution is brought to 1 L with deionized water and mixed, resulting in a pH of approximately 9.2. The buffer is stored at 4° C. for a maximum of 6 weeks.
  • BSA bovine serum albumin solutions
  • a 1% BSA solution in PBS utilized as the second antibody/conjugate diluent, is prepared by adding 1 g BSA (bovine albumin, Fraction V, Sigma Chemical Co.) to 80 ml of PBS, allowing it to stand as it slowly goes into solution, adding PBS to a final volume of 100 ml, and then mixing.
  • This diluent is stored at 4° C. for a maximum of 2 weeks; however if the solution becomes turbid, it is discarded.
  • a 0.025% BSA solution in PBS is prepared fresh for each assay by diluting the 1% BSA diluent with PBS 1:40 (vol/vol).
  • a 5% nonfat dry milk (NFDM) blocking agent is prepared fresh for each assay by adding 5 g nonfat dry milk to 100 ml PBS, mixing well to dissolve, and then vacuum filtering through Whatman #3 filter paper. The solution must be filtered to remove particulates prior to use in blocking.
  • a 2.5% NFDM washing buffer is prepared fresh for each assay by diluting the 5% NFDM solution 1:1 (vol/vol) in PBS. Approximately 800 ml is required per assay plate.
  • the substrate buffer is 0.1M sodium acetate which is brought to a pH of 6.0 with 0.1M citric acid. This buffer is stored at 4° C. for a maximum of 6 weeks.
  • Immulon I REMOVAWELL strips (Dynatech, Chantilly, Va. #011-010-6301) (polystyrene support comprising 96 wells in an 8 row by 12 column format) are assembled in their holders.
  • Antibody from Example 4 or equivalent is diluted to 25 ⁇ g/ml in room temperature coating buffer, and 200 ⁇ l is dispensed into each well. The plate is covered and stored overnight at room temperature.
  • BSA 1% BSA, PBS, and substrate buffer are brought to room temperature. 0.025% BSA, 5% NFDM and 2.5% NFDM are prepared fresh for each assay.
  • Microwells are aspirated with a 12 channel washer.
  • the plate is inverted and blotted on a paper towel to expel residual well contents. 360 ⁇ l 5% NFDM is dispensed per well.
  • the plate is covered and placed in a water-bath at 37° C. for 1 hour.
  • the assay plate is removed from the waterbath and each row of the wells is aspirated in turn. Each row of wells is then filled and aspirated in turn with the multiwell washer until the entire plate has been washed once.
  • Each well is aspirated and then filled with 2.5% NFDM. Each well is then aspirated and the plate blotted forcefully on a paper towel to expel residual well contents. The underside of the plate cover is dried.
  • Diluted samples and standards are added to the plate at 200 ⁇ l/well.
  • the plate is covered and incubated in the 37° C. waterbath for 1 hour.
  • Rabbit anti-HCAVIII protein is diluted to 500 ng/ml in 1% BSA/PBS at room temperature.
  • the assay plate is removed from the waterbath, samples aspirated and the plate is washed three times.
  • the plate is blotted and 200 ⁇ l/well (100 ng/well) of antibody is dispensed.
  • the plate is covered and incubated at 37° C. in the waterbath for 1 hour. Antibody dilution is discarded.
  • Goat anti-Rabbit IgG/Peroxidase conjugate is diluted to 1:32,000 in 1% BSA/PBS at room temperature.
  • the assay plate is removed from the waterbath, aspirated, and washed three times.
  • the plate is blotted, and the conjugate is dispensed at 200 ⁇ l/well.
  • the plate is covered and incubated 1 hour at 37° C. Unused conjugate dilution is discarded.
  • Substrate mix is prepared 10-15 minutes prior to use by first dissolving TMB at a concentration of 10 mg/ml in DMSO. 29.85 ml substrate buffer is dispensed into a 50 ml centrifuge tube. 150 ⁇ l of TMB/DMSO is added and mixed thoroughly. Just prior to use, 50 ⁇ l of the substrate mix is discarded and the substrate mix volume is brought back to 30 ml by adding 50 ⁇ l 3% H 2 O 2 (from a 30% stock diluted 1:10 (vol/vol) in substrate buffer). It is mixed thoroughly, and used immediately.
  • the plate is washed 2 times with 2.5% NFDM and blotted dry.
  • the plate is rewashed 2 times with PBS and blotted dry.
  • 200 ⁇ l/well TMB substrate mix is dispensed, the plate covered, and placed in the dark (drawer or covered box). It is incubated 30 minutes at room temperature.
  • a separate well holder is prepared with one REMOVAWELL strip. 200 ⁇ l of substrate mix is dispensed into three wells, then 200 ⁇ l of deionized water is dispensed into another three wells. These are incubated along with the assay plate.
  • the peroxidase reaction is stopped by adding 50 ⁇ l/well 2M H 2 SO 4 to all wells.
  • the substrate color will shift from blue to yellow when stopped. If necessary, the well contents may be mixed with the 12 channel dispenser prior to reading the results. Acid can also be added to the six wells containing substrate and deionized water.
  • the plate is read with a microplate spectrophotometer reader.
  • Ice cold solutions of ITB (20 mM imidazole, 5 mM Tris, and 0.4 mMpara-nitrophenol, pH 9.4-9.9) and Buffer A (25 mM triethanolamine, 59 mM H 2 SO 4 , and 1 mM benzamidine HCl) are prepared.
  • a homogenate is prepared by scraping with a cell scraper into 1-2 ml of Buffer A a monolayer of tissue cells cultured from a tissue sample taken from a biopsy. A portion of the sample is then boiled to inactivate CA.
  • a tube is placed in an ice water bath.
  • a 10 ⁇ 75 mm glass tubes and rubber stopper with 16 gauge and 18 gauge needle ports is used;
  • a 6 ⁇ 50 mm glass tube and rubber stopper with 18 gauge needle port and 20 gauge needle with attached PE90 tubing is used.
  • the sample is added along with ice cold water to a final volume of 500 ⁇ l for the macroassay or 50 ⁇ l for the microassay.
  • 500 ⁇ l (macro) or 50 ⁇ l (micro) ice cold water is used for a water control.
  • 10 ⁇ l antifoam (A. H. Thomas, Philadelphia, Pa.) is added to the tube which is then incubated in ice water for 0.5 to 3 minutes.
  • the tube is capped with a stopper and CO 2 at 150 ml/min (macro) or 100 ml/min (micro) is bubbled through the smaller needle port for 30 sec.
  • the time at which the solution in the tube becomes colorless is measured and recorded.
  • the tube may be momentarily removed from the bath and held in front of a white background to determine the color change. Comparison to a previously acidified sample may be used.
  • the procedure is repeated with the boiled sample.
  • the volume of sample that corresponds to approximately one enzyme unit is determined using the formula below.
  • VEU volume used ⁇ log2 ⁇ log (boiled time/activated time)
  • One enzyme unit is the activity that halves the boiled control time.
  • the assay is repeated 1-3 times with the sample and boiled sample, using the adjusted volume of sample.

Abstract

The present invention discloses an isolated and purified nucleic acid sequence and corresponding amino acid sequence to a novel protein specific for human lung cancer cells. This gene is expressed at a much higher level in these cells than in normal lung, other normal tissues and other tumor cell lines tested. Also disclosed are two additional recombinant forms of this gene and protein, in the first case a membrane spanning region is removed and in the second case an amino acid is changed by in vitro mutagenesis. Also disclosed are nucleic acid probes for the detection of lung cancer cells from tissue biopsy and body fluids such as serum, sputum and bronchial washings. A method for expressing the antigen in a host cell and its subsequent use as an immunogen in antibody production for test applications is described. An ELISA test to measure shed antigen present in patient samples as well as an enzyme test to measure activity in specimens also is described.

Description

TECHNICAL FIELD
The invention relates to genes and proteins specific for certain cancers and methods for their detection.
BACKGROUND OF THE INVENTION
Lung cancer is the most common form of cancer in the world. Estimates for the year 1985 indicate that there were about 900,000 cases of lung cancer worldwide. (Parkin, et el., "Estimates of the worldwide incidence of eighteen major cancers in 1985," Int J Cancer 1993; 54:594-606). For the United States alone, 1993 projections placed the number of new lung cancer cases at 170,000, with a mortality of about 88%. (Boring, et al., "Cancer statistics," CA Cancer J Clin 1993; 43:7-26). Although the occurrence of breast cancer is slightly more common in the United States, lung cancer is second behind prostate cancer for males and third behind breast and colorectal cancers for women. Yet, lung cancer is the most common cause of cancer deaths.
The World Health Organization classifies lung cancer into four major histological types: (1) squamous cell carcinoma (SCC), (2) adenocarcinoma, (3) large cell carcinoma, and (4) small cell lung carcinoma (SCLC). (The World Health Organization, "The World Health Organization histological typing of lung tumours," Am J Clin Pathol 1982; 77:123-136). However, there is a great deal of tumor heterogeneity even within the various subtypes, and it is not uncommon for lung cancer to have features of more than one morphologic subtype. The term non-small cell lung carcinoma (NSCLC) includes squamous, adenocarcinoma and large cell carcinomas.
Typically, a combination of X-ray and sputum cytology is used to diagnose lung cancer. Unfortunately, by the time a patient seeks medical help for their symptoms, the cancer is at such an advanced state it is usually incurable. Cancer Facts and Figures (based on rates from NCI SEER Program 1977-1981), New York: American Cancer Society, 1986). Routine large-scale radiologic or cytologic screening of smokers has been investigated. Studies concluded that cytomorphological screening did not significantly reduce the mortality rate from lung cancer and was not recommended for routine use. ("Early lung cancer detection: summary & conclusions," Am Rev Respir Dis 1984; 130:565-70). However, in a subpopulation of patients where the cancer is diagnosed at a very early stage and the lung is surgically resectioned, there is a 5-year survival rate of 70-90%. (Flehinger, et al., "The effect of surgical treatment on survival from early lung cancer," Chest; 1992, 101:1013-1018; Melamed, et al,. "Screening for early lung cancer: results of the Memorial Sloan-Kettering Study in New York," Chest; 1984 86:44-53). Therefore, research has focused on early detection of tumor markers before the cancer becomes clinically apparent and while the cancer is still localized and amenable to therapy.
The identification of antigens associated with lung cancer has stimulated considerable interest because of their use in screening, diagnosis, clinical management, and potential treatment of lung cancer. International workshops have attempted to classify the lung cancer antigens into 15 possible clusters that may define histologic origins. (Souhami et al., "Antigens of lung cancer: results of the second international workshop on lung cancer antigens," JNCI 1991; 83:609-612). As of 1988, more than 200 monoclonal antibodies (MAb) have been reported to react with human lung tumors. (Radosevich, et al., "Monoclonal antibody assays for lung cancer," In: Cancer Diagnosis in Vitro Using Monoclonal Antibodies. Edited by H. A. Kupchik. New York: Marcel Dekker, 1988;101-121).
MAbs for lung cancer were first developed to distinguish NSCLC from SCLC. (Mulshine, et al., "Monoclonal antibodies that distinguish nonsmall-cell from small-cell lung cancer," J Immunol 1983; 121:497-502). In most cases, the identity of the cell surface antigen with which a particular antibody reacts is not known, or has not been well characterized. (Scott, et al., "Early lung cancer detection using monoclonal antibodies," In: Lung Cancer. Edited by J. A. Roth, J. D. Cox, and W. K. Hong. Boston: Blackwell Scientific Publications, 1993:310-324).
MAbs have been used in the immunocytochemical staining of sputum samples to predict the progression of lung cancer. (Tockman, et al., "Sensitive and specific monoclonal antibody recognition of human lung cancer antigen on preserved sputum cells: a new approach to early lung cancer detection," J Clin Oncol 1988; 6:1685-1693). In the study, two MAbs were utilized, 624H12 which binds a glycolipid antigen expressed in SCLC and 703D4 which is directed to a protein antigen of NSCLC. Of the sputum specimens from participants who progressed to lung cancer, two-thirds showed positive reactivity with either the SCLC or the NSCLC MAb. In contrast, of those that did not progress to lung cancer, 35 of 40 did not react with the SCLC or NSCLC Mab. This study suggests the need for the development of additional early detection targets to discover the onset of malignancy at the earliest possible stage.
Carcinoembryonic antigen (CEA) is a frequently studied tumor marker of cancer including lung cancer. (Nutini, et al., "Serum NSE, CEA, CT, CA 15-3 levels in human lung cancer," Int J Biol Markers 1990; 5:198-202) . Squamous cell carcinoma antigen is another established serum marker. (Margolis, et al., "Serum tumor markers in non-small cell lung cancer," Cancer 1994; 73:605-609-). Other serum antigens for lung cancer include antigens recognized by MAbs 5E8, 5C7, and 1F10, the combination of which distinguishes between patients with lung cancer from those without (Schepart, et al., "Monoclonal antibody-mediated detection of lung cancer antigens in serum," Am Rev Respir Dis 1988; 138:1434-8), Furthermore, the combination of 5E8, 5C7 and 1F10 was more sensitive, specific and accurate for identifying NSCLC when compared to results from a combination of the CEA and squamous cell carcinoma antigen tests. (Margolis, et al., Cancer 1994; 73:605-609).
Serum CA 125, initially described as an ovarian cancer-associated antigen, has been investigated for its use as a prognostic factor in NSCLC. (Diez, et al., "Prognostic significance of serum CA 125 antigen assay in patients with non-small cell lung cancer," Cancer 1994; 73:1369-76). The study determined that the preoperative serum level of CA 125 antigen is inversely correlated with survival and tumor relapse in NSCLC.
Despite the numerous examples of MAb applications, none has yet emerged that has changed clinical practice. (Mulshine, et al., "Applications of monoclonal antibodies in the treatment of solid tumors," In: Biologic Therapy of Cancer. Edited by V. T. Devita, S. Hellman, and S. A. Rosenberg. Philadelphia: JB Lippincott, 1991, pp. 563-588). MAbs alone may not be the answer to early detection because there has only been moderate success with immunologic reagents for paraffin-embedded tissue. Secondly, lung cancer may express features that cannot be differentiated by antibodies; for example, chromosomal deletions, gene amplification, or translocation and alteration in enzymatic activity.
After the gene to the MAb recognized surface antigen has been cloned, cytogenetic and molecular techniques may provide powerful tools for screening, diagnosis, management and ultimately treatment of lung cancer. An example of a lung cancer antigen that has been cloned is the adenocarcinoma-associated antigen. This antigen, recognized by KS1/4 MAb, is an epithelial malignancy/epithelial tissue glycoprotein from the human lung adenocarcinoma cell line UCLA-P3. (Strnad, et al., "Molecular cloning and characterization of a human adenocarcinoma/epithelial cell surface antigen complementary DNA," Cancer Res 1989; 49:314-317). The antigen has been found on all adenocarcinoma cells tested and in various corresponding normal epithelial cells. Northern blot analysis indicated that transcription of the adenocarcinoma-associated antigen was detected in RNA isolated from normal colon but not in RNA isolated from normal lung, prostate, or liver. Therefore identification of adenocarcinoma-associated antigen in lung cells may prove to be diagnostic for adenocarcinoma.
The cloning of CEA and the nonspecific crossreacting antigen (NCA) has allowed the development of specific DNA probes which discriminate their expression in lung cancer at the mRNA level. (Hasegawa, et al., "Nonspecific crossreacting antigen (NCA) is a major member of the CEA-related gene family expressed in lung cancer," Br J Cancer 1993; 67:58-65). NCA is a component of the CEA gene family in lung cancer and is also recognized by anti-CEA antibodies, especially polyclonal antibodies. Because of the crossreactivity, investigations to analyze CEA and NCA separately in lung disease had been difficult. The use of DNA probes determined that lung cancer cells fall into three different types according to their CEA and/or NCA expression by Northern blot analysis. Specifically, lung cancers expressed both CEA and NCAmRNA, only NCAmRNA, or neither mRNA. CEA-relatedmRNA expression was always accompanied by NCAmRNA expression and there were no cases of CEAmRNA expression alone. The separate assessment of CEA and NCA expression in lung cancers may be important in determining the prognosis of lung cancers because the antigens have been described as cell-cell adhesion molecules and may play a role in cancer metastasis.
Another method to detect the presence of an antigen gene or its mRNA in specific cells or to localize an antigen gene to a specific locus on a chromosome is in situ hybridization. In situ hybridization uses nucleic acid probes that recognize either repetitive sequences on a chromosome or sequences along the whole chromosome length or chromosome segments. By tagging the probes with radioisotopes or color detection systems, chromosome regions can be identified within the cell. Investigations using in situ hybridization have demonstrated numerous chromosomal abnormalities in samples from human tumors, including bladder, neuroectodermal, breast, gastric and lung cancer tumors. (Kim, et al., "Interphase cytogenetics in paraffin sections of lung tumors by non-isotopic in situ hybridization. Mapping Genotype/phenotype heterogeneity," Am J Pathol 1993; 142:307-317).
Fluorescent in situ hybridization (FISH) allows cells to be stained so that genetic aberrations resulting in changes in gene copy number or structure can be quantitated by fluorescent microscopy. In this technique, a chemically labeled single-stranded nucleic acid probe homologous to the target nucleic acid sequence is annealed to denatured nucleic acid contained in target cells. The cells may be mounted on a microscope slide, in suspension or prepared from paraffin-embedded material. Treating the chemically modified probes with a fluorescent ligand makes the bound probe visible. FISH has been used for (1) detection of changes in gene copy number and gene structure; (2) detection of genetic changes, even in low frequency subpopulations; and (3) detection and measurement of the frequency of residual malignant cells. (Gray, et al., "Molecular cytogenetics in human cancer diagnosis," Cancer 1992; 69:1536-1542).
Other molecular markers for lung cancer include oncogenes and tumor suppressor genes. Dominant oncogenes are activated by mutation and lead to deregulated cellular growth. Such genes code for proteins that function as growth factors, growth factor receptors, signal transducing proteins and nuclear proteins involved in transcriptional regulation. Amplification, mutation, and translocations have been documented in many different cancer cells and have been shown to lead to gene activation or overexpression.
The ras family of oncogenes comprises a group of membrane associated GTP-binding proteins thought to be involved in signal transduction. Mutations within the ras oncogenes, resulting in sustained growth stimulation, have been identified in 15 to 30% of human NSCLC. (Birrer, et al., "Application of molecular genetics to the early diagnosis and screening of lung cancer," Cancer 1992; 52suppl; 2658s-2664s). Patients with tumors containing ras mutations had decreased survival compared with patients whose tumors had no ras mutations. Polymerase chain reaction (PCR) amplification of ras genes can be analyzed to determine the presence of mutations by several methods: (a) differential hybridization of 32 P-labeled mutated oligonucleotides; (b) identification of new restriction enzyme sites created by the activating mutation; (c) single-strand conformational polymorphisms; and (d) nucleic acid sequencing. These methods combined with PCR technology could allow detection of an activated ras gene from sputum specimens.
Another family of dominant oncogenes, the erb B family, has been found to be abnormally expressed in lung cancer cells. This group codes for membrane-associated tyrosine kinase proteins and contains erb B1, the gene coding for the epidermal growth factor (EGF) receptor, and erb B2 (also called Her-2/neu). The erb B1 gene has been found to be amplified in NSCLC (up to 20% of squamous cell tumors), while the EGF receptor has been shown to be overexpressed in many NSCLC cells (approximately 90% of squamous cell tumors, 20 to 75% of adenocarcinomas, and rarely in large cell or undifferentiated tumors). (Birrer, et al., Cancer 1992:52 suppl; 2658s-2664s). Amplification of the related oncogene erb B2 (Her-2/neu) occurs infrequently in lung cancer but is a negative prognostic factor in breast cancer. However, overexpression of the erb B2 protein product, p185neu, occurs in some NSCLC and may be related to poor prognosis. (Kern, et al., "p185neu expression in human lung adenocarcinomas predicts shortened survival," Cancer Res 1990; 50:5184-5191).
A third family of dominant oncogenes involved in lung cancer is the myc family. These genes encode nuclear phosphoproteins, which have potent effects on cell growth and which function as transcriptional regulators. Unlike ras genes, which are activated by point mutations in lung cancer cells, the myc genes are activated by overexpression of the cellular myc genes, either by gene amplification or by rearrangements, each ultimately leading to increased levels of myc protein. Amplification of the normal myc genes is seen frequently in SCLC and rarely in NSCLC.
The loss or inactivation of tumor suppressor genes may also be important steps in the pathway leading to invasive cancer. Tumor suppressor genes function normally to suppress cellular proliferation, and since they are recessive oncogenes, mutations or deletions must occur in both alleles of these genes before transformation occurs.
A phosphoprotein p53, which is encoded by a gene located on chromosome 17p, suppresses transformation in its wild-type state. While in its mutant state, p53 acts as a dominant oncogene. p53 functions in DNA binding and transcription activation. Mutations of p53 have been found in many human cancers including colon, breast, brain and lung cancer cells. (Birrer, et al., Cancer Res.(suppl) 1992, 52:2658s-2664s). In NSCLC cell lines, p53 mutations have been found at a rate of up to 74%. (Mitsudomi, et al., "p53 gene mutations in non-small-cell lung cancer cell lines and their correlation with the presence of ras mutations and clinical features," Oncogene 1992; 7:171-180).
Despite all of the advances made in the area of lung cancer, medical and surgical intervention has resulted in little change in the 5-year survival rate for lung cancer patients. Early detection holds the greatest hope for successful intervention. There remains a need for a practical method to diagnose lung cancer as close to its inception as possible. In order for early detection to be feasible, it is important that specific markers be found and their sequences elucidated.
A lung cancer marker antigen, specific for NSCLC, has now been found, sequenced, and cloned. The antigen is useful in methods for detection of non-small cell lung cancer and for potential production of antibodies and probes for treatment compositions.
BRIEF DESCRIPTION OF THE DRAWING
FIGURE 1 depicts the alignment of the amino acid sequence of HCAVIII with Previously described carbonic anhydrases. Conserved amino acids are shown in bold.
SUMMARY OF THE INVENTION
The invention concerns a lung cancer antigert (HCAVIII) gens specific for non-small cell lung cancer.
In one embodiment, the invention relates to an isolated substantially purified nucleic acid encoding the protein sequence shown in SEQ ID NO:2, and may be mRNA.
In other embodiments, the invention relates to cDNAs which encode a protein having a signal sequence (SEQ ID NO:2), or the mature form of the protein (SEQ ID NO:4), or a truncated form of the protein lacking the transmembrane domain (SEQ ID NO:10), or a protein in which one or more amino acids in the phosphorylation region of the protein have been altered to affect that function, an example of which is shown in SEQ ID NO:13.
In other embodiments, proteins encoded by the cDNA of SEQ ID NO:1, or SEQ ID NO:3 or SEQ ID NO:9, or a cDNA altered in the phosphorylation region, an example of which is SEQ ID NO:12, are provided.
In another aspect, the invention relates to a transcribable recombinant DNA clone for HCAVIII.
In further aspects of the invention, expression vectors for HCAVIII and modifications thereof are an object.
The invention further relates to methods of detection of lung cancer.
In one aspect an in situ hybridization technique is provided. In another aspect, a fluorescence in situ hybridization technique is provided. In a further aspect, an ELISA assay is provided. In another aspect, detection of carbonic anhydrase activity which correlates with lung cancer antigen is provided.
DETAILED DESCRIPTION OF THE INVENTION
The nucleic acid sequence coding for a cell surface protein (said protein hereinafter designated HCAVIII) which is highly specific for non-small cell lung cancer cells has now been obtained. This gene sequence will facilitate detection and treatment of the disease, which to date has often proven difficult.
The HCAVIII cDNA in the vector pLC56 has been sequenced and characterized including the entire coding region and substantially all of the upstream and downstream non-translated regions. The cDNA in pLC56 was sequenced on both strands from exonuclease III-generated deletions and subsequent subcloning into M13 vectors or directly from the cloning vectors using the di-deoxy method and a SEQUENASE ® Version 2.0 kit (U.S. Biochemicals, Cleveland, Ohio). Additional regions of DNA were subcloned as small restriction fragments into the same vectors for sequence analysis. Overlapping segments were ordered using MacVector Align software (Kodak/IBI Technologies, New Haven Conn.). SEQ ID NO:1 represents the cDNA encoding HCAVIII and a presumed signal peptide. SEQ ID NO:2 represents the signal peptide (amino acid residues -29 to -1) followed by the mature protein (amino acid residues 1 to 325). As predicted from the cDNA sequence in pLC56, a protein of about 354 amino acids is encoded with the predictive size of 39448 daltons. A hydrophilicity plot (MacVector software, Kodak/IBI Technologies) of this protein provided strong evidence of a leader peptide at the N-terminus and a membrane-spanning segment near the C-terminus. The membrane-spanning segment provides evidence that this protein is membrane bound, as also predicted by its positive selection with panning methodology (See Watson, et al., Recombinant DNA, 2nd ed., pp. 115-116, 1992). The cleavage site of the signal as predicted by yon Heijne (yon Heijne, Gunnar, Nucleic Acids Res 1986; 14:4683-4690) is 29 amino acids down from the N-terminus methionine. SEQ ID NO:3 corresponds approximately to the coding region of the mature polypeptide. The subsequent "mature" protein is proposed to be 325 amino acids, initiating with serine, and of a calculated 36401 daltons and a pI of 6.42 (SEQ ID NO:4).
Homology searches against NCBI BlastN or BlastX version 1.3.12MP (National Center for Biotechnology Information, Bethesda, Md.) provided evidence that the gene and protein are novel, not previously identified in either database. (Altschul, et al., "Basic local alignment search tool," J Mol Biol 1990; 215:403-410). Additional searches against another database (Entrez, version 9) gave similar results. Alignment searches indicated this protein shares common features with the seven human carbonic anhydrase proteins previously identified. However, as described below, certain structural features distinct to HCAVIII exist that may confer unique properties to this protein and a possible role in the transformation pathway to tumorgenicity. This group of enzymes catalyze the hydration of carbon dioxide
CO.sub.2 +H.sub.2 O⃡HCO.sub.3 +H.sup.+
and in reverse the dehydration of HCO3 -. This protein is identified as a carbonic anhydrase (CA) based on the conservation of amino acids at positions critical for the binding of Zn+2, critical for the catalysis of CO2, as well as numerous other conserved amino acids (see FIG. 1). The protein is 34 to 64 amino acids longer (at the C-terminus) than any previously reported carbonic anhydrase by virtue of the membrane-spanning region, also found in HCAIV and an additional approximate 30 amino acids on the cytoplasmic side of the cell, which are apparently missing in other human CA isoforms. In addition, this intracellular domain contains a phosphorylation site recognized by protein kinase C and other kinases, as defined by the motif "Arg--Arg--Lys--Ser" (SEQ ID NO:5 and SEQ ID NO:6) (amino acid residues 1-4 in SEQ ID NO:6 and amino acid residues 299-302 in SEQ ID NO:2 and SEQ ID NO:4). Interestingly, this motif is found only in HCAVIII, and at a functionally significant site, i.e., within the cytosol. A surface cleft essential for enzymatic function present on other carbonic anhydrases is conserved for this protein, suggesting this protein will confer enzymatic activity. HCAVI has been isolated from sheep salivary glands in a dimer conformation, by virtue of intermolecular disulfide bonds derived from cysteines at positions conserved in sheep and human HCAVI as well as the protein encoded by pLC56, but not other human CA's. Consequently, HCAVIII is likely presented on the cell surface as a dimer of a predicted 72804 daltons. In addition, five possible N-glycosylation sites are predicted by the primary amino acid sequence and the motif "Asn--Xaa--Ser (Thr)", beginning at amino acid residues -2, 51, 133, 151, and 202 in SEQ ID NO:2, respectively.
HCAVIII is expressed at a much higher level in a non-small cell lung cancer cell line (A549) than in normal lung tissue, other normal tissues, and other tumor cell lines which makes it useful in distinguishing this disease. This is clearly demonstrated in Table 1. Data for this table was obtained as follows. Total cellular RNA was isolated from the indicated actively growing cell lines as described by Chirgwin, et al., "Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease," Biochemistry 1979; 18:5294-5299. RNA samples were fractionated over a 1% agarose-formaldehyde gel and transferred to a nylon membrane (Qiagen, Chatsworth, Calif.) by capillary action. The hybridization probe was generated from a 1 kilobase pair BstXI restriction fragment isolated from pLC56, a plasmid harboring the HCAVIII gene in its initial isolation. This fragment was radiolabeled with 32 p using a PRIME-IT® Random Primer Labeling Kit obtained from Stratagene, La Jolla, Calif. A membrane containing RNA derived from healthy human tissue was purchased from Clonetech Laboratories, Inc., Palo Alto, Calif. RNA blots were hybridized in a standard cocktail containing 32 P-labeled probe at 42° C. overnight then exposed to X-ray film. The same blots were subsequently, upon removal of the probe, rehybridized with a second 32 P-labeled DNA from β-actin to serve as a positive control for integrity of the blotted RNA.
As shown in Table 1, normal lung tissue does not express the HCAVIII gene in detectable amounts. Other tumor cell lines fail to express, or express only in minor amounts, which will allow easy distinction of non-small cell carcinomas.
              TABLE 1                                                     
______________________________________                                    
NORTHERN BLOTS USING HCAVIII cDNA AGAINST                                 
NORMAL TISSUES AND TUMOR CELL LINES                                       
TISSUE           mRNA (kB)    INTENSITY                                   
______________________________________                                    
NORMAL TISSUE                                                             
heart            nd.sup.1     --                                          
brain            4.5          1X.sup.2                                    
placenta         4.5          1X                                          
lung             nd           --                                          
liver            nd           --                                          
skeletal muscle  nd           --                                          
kidney           4.5          100X                                        
pancreas         4.5          10X                                         
TUMOR CELL LINE                                                           
A549 (lung carcinoma)                                                     
                 3.5          5000X                                       
                 5.4          50X                                         
                 8.0          25X                                         
                 9.0          25X                                         
BT20 (breast carcinoma)                                                   
                 nd           --                                          
G361 (melanoma)  nd           --                                          
HT144 (melanoma) nd           --                                          
U937 (histiocytic lymphoma)                                               
                 nd           --                                          
KG-1 (myelogenous leukemia)                                               
                 nd           --                                          
______________________________________                                    
 .sup.1 nd = none detected                                                
 .sup.2 1X = at limit of detection
In one embodiment of the invention, probes are made corresponding to sequences of the cDNA shown in SEQ ID NO:3, which are complimentary to the mRNA for HCAVIII. These probes can be radioactively or non-radioactively labeled in a number of ways well known to the art. The probes can be made of various lengths. Such factors as stringency and GC content may influence the desired probe length for particular applications. The probes correspond to a length of 10-986 nucleotides from SEQ ID NO:3. The labeled probes can then be bound to detect the presence or lack of mRNA encoding HCAVIII in biopsy material through in situ hybridization. The mRNA is expected to be associated with the presence of non-small cell tumors and to be a marker for the precancerous condition as well.
In situ hybridization provides a specificity to the target tissue that is not obtainable in Northern, PCR or other probe-driven technologies. In situ hybridization permits localization of signal in mixed-tissue specimens commonly found in most tumors and is compatible with many histologic staining procedures. This technique is comprised of three basic components: first is the preparation of the tissue sample provided by the pathologist to permit successful hybridization to the probe. Second is the preparation of the hybridization probe, typically a RNA complementary to the mRNA of the gene of interest (i.e., antisense RNA). RNA probes are preferred over DNA probes for in situ hybridizations mainly because background hybridization of the probe to irrelevant nucleic acids or nonspecific attachment to cell debris or subcellular organelles can be eliminated with RNAse treatment post-hybridization. Third is the hybridization and method of detection post-hybridization. Typically the RNA transcript probe has been radiolabeled by the incorporation of 32 p or 35 S nucleotides to permit subsequent detection of the probed specimen by autoradiography or quantitation of silver grains following treatment with autoradiographic emulsion. Nonradioactive detection systems have also been developed. In one example, biotinylated nucleotides can be substituted for the radioactive nucleotide in the RNA probe preparation, permitting visualization of the probed sample by immunocytochemistry-derived techniques. Example 1 describes in situ hybridization procedures using RNA probes derived from the HCAVIII gene, and Example 2 provides exemplary fluorescent in situ (FISH) hybridization procedures.
The cDNA for HCAVIII (SEQ ID NO:3) is currently in an expression vector which is be used to generate the protein in E. coli. This expression system described in Example 3 produces HCAVIII to be used as an antigen for the generation of antibodies (Example 4) for use in an ELISA assay to detect shed HCAVIII in body fluids as described in Example 5. The methods for production of antibodies and ELISA type assays are well known in the art. Exemplary methods and components of these procedures have been chosen and developed and are described in Examples 4 and 5.
The expression and purification of foreign proteins in E. coli is often problematic. On occasion, the protein is expressed at high levels but is deposited within the cell as an insoluble, denatured form termed an inclusion body. These bodies are often observed when the foreign protein contains a hydrophobic domain, such as found in the membrane spanning segment of HCAVIII. Through recombinant DNA technology, the DNA sequences encoding the membrane spanning segment of HCAVIII are deleted. The protein expressed in E. coli from this engineered plasmid is now in a soluble and native form within the cell, permitting a rapid and less harsh purification. In addition, the ELISA test to measure HCAVIII shed into body fluids as described in Example 5 relies on the recombinant protein produced from E. coli. Typically, the shed antigen is a membrane-bound receptor that has been released from the membrane spanning segment anchoring it to the cell. Consequently, the recombinant HCAVIII engineered to remove the membrane spanning segment is a more accurate representation of the putative HCAVIII shed antigen found in specimens and may prove to be the preferred antigen for polyclonal antisera and monoclonal antibody production as described for the development of an ELISA test. To produce the engineered plasmid, a first plasmid is constructed by cleaving pLC56 with the restriction enzyme Tth111 I, followed by treatment with T4 -DNA polymerase and dGTP, and finally with alkaline phosphatase to remove 5'-terminal phosphates. The DNA sample is then purified by phenol/chloroform extraction and ethanol precipitation. The sample is digested with the restriction endonuclease BspE1, then the fragments are resolved by agarose gel electrophoresis to permit the isolation of a 267 base pair fragment. A second plasmid described previously for expression of the HCAVIII mature protein (SEQ ID NO:4), is cleaved with EcoRI and BspE1 followed by alkaline phosphatase treatment and purification by phenol/chloroform extraction and ethanol precipitation. Two oligonucleotides are synthesized, being 5'-TGAGTCGACG (SEQ ID NO:7) and 5'-AATTCGTCGACTCA (SEQ ID NO:8), that complement each other and upon annealing, provide a termination codon (TGA) and sequence complementary to EcoRI cleaved DNA. Finally, the two oligonucleotides, the 267 base pair fragment, and the BspEI/EcoRI cleaved plasmid will be combined in a ligation reaction, and the resultant plasmid which contains the truncated DNA sequence (SEQ ID NO:9) are used to transform competent E. coli. Upon expression in E. coli, the resulting truncated protein (SEQ ID NO:10) is 271 amino acids and of a size consistent with other HCA's but lacking the membrane spanning segment and the intracellular domain.
An understanding of protein phosphorylation and its role in the mechanism of cell transformation has been actively pursued, most notably with tyrosine phosphorylation and oncogene activation. The role of serine/threonine protein phosphorylation by a variety of protein kinases including protein kinase C has been studied extensively with respect to signal transduction, but its role in oncogenesis is less clear. To provide a valuable tool to be used in the study of the role of HCAVIII serine phosphorylation in oncogenesis, an altered cDNA can be prepared to code for an altered protein. Changes to amino acids other than "Gly" may be realized by alterations of the oligonucleotide sequence (SEQ ID NO:11) to encode the selected residue. Other modifications to alter the serine phosphorylation site would utilize the described technology to modify either both "Arg" residues located within SEQ ID NO:6 or amino acid residues 299 and 300 of SEQ ID NO:4. Since "Arg" residues contain a net positive charge, the substituted amino acids would preferably be "Lys" or "His," also positively charged amino acids. An exemplary plasmid is produced in which the "Ser" codon (amino acid residue 4 of SEQ ID NO:6; amino acid residue 302 in SEQ ID NO:2 and SEQ ID NO:4), is converted to a "Gly" codon using an in vitro mutagenesis technique described in Example 3 and previously recited in Kunkel, Thomas, "Rapid and efficient site-specific mutagenesis without phenotypic selection," Proc Natl Acad Sci USA 1985; 82:488-492, and the oligonucleotide 5'-CTTTTTTGATACCCTTCCTTCTGAA (SEQ ID NO:11) (located in SEQ ID NO:1 at the base pairs 1010-1034 with 1022 as the mutagenized base pair). The DNA sequences containing the HCAVIII gene engineered for production of the mature protein and mutagenized codon is released from the mutagenesis vector by BamHI and EcoRI restriction endonucleases and ligated into pGEX4T1 cleaved with the same enzymes, and the resultant plasmid is used to transform competent E. coli. The codon mutagenesis is confirmed by DNA sequence analysis, and the protein is expressed and purified from E. coli as described in Example 3. The DNA sequence of the altered plasmid as shown in SEQ ID NO:12 differs from the gene encoding the mature protein (SEQ ID NO:2) in that the nucleotide 1022 (nucleotide 904 in SEQ ID NO:12) is changed from "A" to "G" and the protein sequence (SEQ ID NO:13) expressed by the altered plasmid is identical to the mature protein (SEQ ID NO:4) except that amino acid residue 302 is changed from "Ser" to "Gly."
Another way to detect the presence of increased HCAVIII could be to assay for levels of carbonic anhydrase activity in biopsy materials as described in Example 6. This should be a useful test as HCAVIII, although it is an immunologically unique molecule, contains small but distinct regions which are conserved between previously reported carbonic anhydrase proteins.
In another embodiment of the invention, primers are made complimentary to the HCAVIII cDNA (SEQ ID NO:3) for detecting expression of the gene. PCR amplification of cDNA from lung biopsy cells would indicate the presence of the same non-small cell lung carcinoma.
Due to the non-small cell lung cancer specificity of HCAVIII and the gene encoding the protein, antibodies specific for HCAVIII would also exhibit non-small cell lung cancer specificity which can be employed for diagnostic detection of HCAVIII in body fluids such as serum or urine or HCAVIII containing cells. Targeting of cancer therapeutic drugs to HCAVIII containing cells can also be developed using HCAVIII specific antibodies. The genetic expression of the gene encoding HCAVIII could be modulated by drugs or anti-sense technology resulting in an alteration of the cancer state of the HCAVIII containing cells.
Example 1 In Situ Hybridization Using RNA Probes Derived from the HCAVIII Gene
Tissue samples are treated with 4% paraformaldehyde (or an equivalent fixative), dehydrated in sequential ethanol solutions of increasing concentrations (e.g., 70%, 95% and 100%) with a final xylene incubation (see Current Protocols in Molecular Biology, pp. 14.01-14.3 and Immunocytochemistry II:IBRO Handbook Series: Methods in the Neurosciences Vol 14; pp 281-300, incorporated herein by reference). The tissue is embedded in molten paraffin, molded in a casting block and can be stored at room temperature. Tissue slices, typically 8 μm thick, are prepared with a microtome, dried onto gelatin-treated glass slides and stored at -20° C.
DNA sequences from the HCAVIII gene (SEQ ID NO:3) are subcloned into a plasmid engineered for production of RNA probes. In this example, a 776 bp DNA fragment is released from a pLC56 plasmid following BamHI/AccI digestion, where the BamHI site has been created by in vitro mutagenesis (see E. coli expression below). This fragment is ligated into pGEM-2 (Promega Biotec, Madison, Wis.) that was cleaved with BamHI and AccI and transformed into competent E. coli. This constructed plasmid contains the T7 RNA polymerase promoter downstream of the AccI restriction site and hence can drive transcription of the antisense HCAVIII sequences defined by the BamHI/AccI fragment. Following linearization of the subsequent plasmid with BamHI, an in vitro transcription reaction composed of transcription buffer (40 mM Tris-HCl, pH 7.5, 6 mMMgCl2, 2 mM spermidine, 10 mM NaCl, 10 mM dithiothreitol, 1 u/ul ribonuclease inhibitor), linearized plasmid, 10 mM GTP, 10 mM ATP, 10 mM CTP, 100 μCi of (35 S)UTP, and T7 RNA polymerase is incubated at 37° C. Multiple RNA copies of the gene are produced that are used as a hybridization probe. The reaction is terminated by the addition of DNase, and the synthesized RNA is recovered from unincorporated nucleotides by phenol/chloroform extraction and sequential ethanol precipitations in the presence of 2.5M ammonium acetate.
The slides containing fixed, sectioned tissues are rehydrated in decreasing concentrations of ethanol (100%, 70% and 50%), followed by sequential treatments with 0.2N HCl, 2X SSC (where 20X SSC is 3M NaCl and 0.3M sodium citrate) at 70° C. to deparaffinate the sample, phosphate buffered saline (PBS), fixation in 4% paraformaldehyde and PBS wash. The slides are blocked to prevent nonspecific binding by the sequential additions of PBS/10 mM dithiothreitol (45° C.), 10 mM dithiothreitol/0.19% iodoacetamide/0.12% N-ethylmaleimide and PBS wash. The slides are equilibrated in 0.1M triethylamine, pH 8.0, followed by treatment in 0.1M triethylamine/0.25% acetic anhydride and 0.1M triethylamine/0.5% acetic anhydride and washed in 2X SSC. The slides are then dehydrated in increasing concentrations of ethanol (50%, 70% and 100%) and stored at -80° C.
A hybridization mix is prepared by combining 50% deionized formamide, 0.3M NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1X Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, 0.02% bovine serum albumin (BSA)), 500 μg/ml yeast tRNA, 500 μg/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000 and the 35 S-labeled RNA probe. This solution is placed on the fixed, blocked tissue slides which are then incubated at 45° C. in a moist chamber for 0.5 to 3 hours. The slides are washed to remove unbound probe in 50% formamide, 2X SSC, 20 mM 2-mercaptoethanol (55° C.), followed by 50% formamide, 2X SSC, 20 mM 2-mercaptoethanol and 0.5% Triton-X 100 (50° C.) and finally in 2X SSC/20 mM 2-mercaptoethanol (room temperature). The slides are treated with 10 mM Tris-HCl, pH 8.0/0.3M NaCl/40 μg/ml RNase A/2 μg/ml RNAse T1 (37° C.) to reduce levels of unbound RNA probe. Following RNAse treatment, the slides are washed in formamide/SSC buffers at 50° C., and room temperature and then dehydrated in increasing ethanol concentrations containing 0.3M ammonium acetate, and one final 100% ethanol wash. The slides are then exposed to X-ray film followed by emulsion autoradiography to detect silver grains.
Test tissue samples are compared to matched controls derived from normal lung tissue. Evidence of elevated transcription of the HCAVIII gens in test tissue compared to normal tissue, as determined by autoradiography (X-ray film) or alternatively by the quantitation of silver grains following emulsion autoradiography would provide evidence of a positive diagnosis for lung cancer.
Example 2 Fluorescent In Situ Hybridization (FISH) Using DNA Probes Derived from the HCAVIII Gene
A genomic clone to the HCAVIII gens (SEQ ID NO:1) is isolated using a PCR primer pair which have been identified from the pLC56 cDNA sequence. This primer pair is located in putative exon 6 of the pLC56 gens, and they are identified as Probe Exon 6A (5'-ACATTGAAGAGCTGCTTCCGG-3'; SEQ ID NO:14) and Probe Exon 6B (5'-AATTTGCACGGGGTTTCGG-3'; SEQ ID NO:15). The genomic clone of HCAVIII is then identified as a PCR product of about 119 bp using this primer pair from the designated genomic clone. This result is confirmed by Southern blotting and DNA sequence analysis.
The DNA probe comprising the genomic clone of HCAVIII plus flanking sequences is labeled in a random primer reaction with digoxigenin-11-dUTP (Boehringer Mannheim Biochemicals, Indianapolis, Ind.) by combining the DNA with dNTP(-TTP, final 0.05 mM), digoxigenin-11-dUTP/dTTP (0.0125 mM and 0.0375 mM, final), 10 mM 2-mercaptoethanol, 50 mM Tris-HCl, pH 7.5, 10 mMMgCl2, 20 U of DNA polymerase I and 1 ng/ml DNase. The reaction is incubated at 15° C. for two hours, and then terminated by adding EDTA to a final concentration of 10 mM. The labeled DNA probe is further purified by gel filtration chromatography. It is apparent to those skilled in the art that other suitable substrates such as biotin-11-dUTP can be substituted for digoxigenin-11-dUTP in the procedure above.
A hybridization mix is prepared by combining 50% deionized formamide, 0.3M NaCl, 10 mMTris-HCl, pH 8.0, 1 mM EDTA, 1X Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, and 0.02% bovine serum albumin), 500 μg/ml yeast tRNA, 500 μg/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000, and the labeled DNA probe.
Single cell suspensions of tissue biopsy material or normal tissue are fixed in methanol/glacial acetic acid (3:1 vol/vol) and dropped onto microscope slides. (Aanastasi, et al., "Detection of Trisomy 12 in chronic lymphocytic leukemia by fluorescent in situ hybridization to interphase cells: a simple and sensitive method," Blood 1992; 77:2456-2462). After the slides are heated for 1-2 hours at 60° C., the hybridization mix is applied to the slides which are then incubated at 45° C. in a moist chamber for 0.5-3 hours. After incubation, the slides are washed three times with a solution comprising 50% formamide and 2X SSC at 42° C., washed twice in 2X SSC at 42° C., and finally washed in 4X SSC at room temperature. The slide is blocked with a solution of 4X SSC and 1% BSA, and then washed with a solution of 4X SSC and 1% Triton X-100.
The hybridized digoxigenin-labeled probe is detected by adding a mixture of sheep anti-digoxigenin antibody (Boehringer Mannheim) diluted in 0.1M sodium phosphate, pH 8.0, 5% nonfat dry milk, and 0.02% sodium azide, followed by the addition of fluorescein-conjugated rabbit anti-sheep IG for detection. The slides are then washed in PBS, mounted in Vectashield (Vector Laboratories, Inc., Burlingame, Calif.), and viewed by fluorescent microscopy.
Hybridization signals are enumerated in tumor derived tissue and then compared to normal tissue. Normal tissue displays two distinct hybridization signal characteristics of a diploid state. Enumeration over the rate of two hybridization signals/cell is considered significant.
Example 3 Expression of HCAVIII
Expression of foreign proteins is often performed in E. coli when an immunogen or large amounts of protein are desired, as in the development of a diagnostic kit. A preferred system for E. coli expression has been described (Smith, et al., "Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione-s-transferase," Gene 1988; 67:31-40) whereby glutathione transferase is expressed with amino acids representing the cloned protein of interest attached to the carboxylterminus. The fusion protein can then be purified via affinity chromatography and the protein of interest fused to glutathione transferase released by digestion with the protease thrombin or alternatively the fusion protein is released intact from the affinity column by competing levels of free glutathione.
To express the HCAVIII protein (SEQ ID NO:4) of this invention in E. coli using the above described technology, an expression plasmid was produced in which the glutathione transferase gene was fused in frame with the HCAVIII gene (SEQ ID NO:1) to produce a fusion protein. The fusion gene/expression plasmid was assembled from nucleic acids derived from the following sources. First, the expression plasmid pGEX4T1 (Pharmacia, Piscataway, N.J.) was cleaved in the polycloning region with the restriction endonucleases BamHI and EcoRI to permit insertion of the HCAVIII gene. Second, an oligonucleotide was synthesized, being 5'-GTCCACTTGGATCCGTTCACTGG-3' (SEQ ID NO:16). Using the in vitro mutagenesis procedure described by Kunkel (Proc Natl Acad Sci USA 1985; 82:488-492) and the above oligonucleotide, a BamHI restriction site was created without altering the amino acid codons of the original protein. In addition the created BamHI site was situated in correct reading frame and proximity to the predicted cleavage site separating the signal peptide from the mature protein. The DNA sequences encoding the mature protein were released from the mutagenesis vector as a BamHI/EcoRI fragment, where the EcoRI site originates from a polycloning region of the DNA sequencing vector pUC19 found downstream of the HCAVIII gene. The DNA fragments described above comprised of pGEX4T-1 cleaved at BamHI and EcoRI and the HCAVIII gene released as a BamHI/EcoRI fragment were combined in a mixture composed of 1X T4 ligase buffer (50 mM Tris-HCl, 10 mMMgCl2, 20 mM dithiothreitol, 1 mMATP, 50 μg/ml BSA, final pH 7.5) and T4 DNA ligase (New England Biolabs, Beverly, Mass.). The ligated DNA was used to transform a suitable strain of E. coli such as XL-1 Blue (Stratagene). The recovered plasmid is sequenced to confirm the expected DNA sequence. Protein expression is induced in E. coli with the chemical isopropyl β-thiogalactoside, and the fusion protein is released by cell lysis, binding to an affinity column composed of glutathione-agarose (Sigma, St. Louis, Mo.) and cleavage with thrombin to release the HCAVIII protein. The resulting protein is suitable as an immunogen for polyclonal or monoclonal antibody production and for usage in an ELISA kit as an internal standard and positive control.
The length of the resulting protein can be varied by altering the length of SEQ ID NO:1 prior to insertion into the expression plasmid, or by cleavage of amino acids from the protein resulting in the above example. Structure/function studies of other HCA's suggest modifications (as defined by deletions at the N-terminal and C-terminal) more extensive than disclosed in SEQ ID NO:9 would still permit the production and use of a protein as an immunogen or standard, these deletions being a protein defined by about amino acid residue 3 to amino acid residue 259 in SEQ ID NO:9. Using existing technology one could synthesize a peptide of approximately 10 to 40 amino acids in length that comprises a structural domain of HCAVIII. This synthesized peptide, coupled to a carrier protein, could be used for generating polyclonal antisera specific for native HCAVIII.
Example 4 Production of Antibodies to HCAVIII
The production of polyclonal antisera is described in great detail in Harlow, et al., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, 1988 incorporated herein by reference. The HCAVIII protein (SEQ ID NO:4) in the presence of an adjuvant is injected into rabbits with a series of booster shots in a prescribed schedule optimal for high titers of antibody in serum.
An extensive description for producing monoclonal antibodies derived from the spleen B cells of an immunized mouse and an immortalized myeloma cell is found in the above reference for polyclonal antisera production. Mice are immunized with either the purified HCAVIII protein or a glutathione/HCAVIII fusion protein. Following cell fusion, selection for hybrid cells' and subcloning, hybridomas are screened for a positive antibody against whole A549 cells or purified HCAVIII protein using an indirect ELISA assay as described for the ELISA kit (see Example 5).
Example 5 ELISA Assay of Shed HCAVIII
An indirect ELISA screening assay for HCAVIII protein (SEQ ID NO:4) has been designed to detect and monitor the HCAVIII protein in body fluids including but not limited to serum and other biological fluids such as sputum or bronchial effluxion at effective levels necessary for sensitive but accurate determinations. It is intended to aid in the early diagnosis of non-small cell cancer, for which there currently is no effective treatment. An early-detection, accurate, non-invasive assay for non-small cell lung cancer would be of great benefit in the management of this disease.
The immunochemicals used in this procedure are rabbit anti-human HCAVIII antibody (purified IgG, IgM) which is produced according to the procedure given in Example 4, mouse anti-human HCAVIII (monoclonal) also produced according to the procedure given in Example 4, and goat anti-Rabbit IgG/peroxidase conjugate. The HCAVIII protein standard and internal positive control are produced as described in Example 3 for expression in E. coli.
Substrate components include 2M H2 SO4 stored at room temperature; dimethylsulfoxide (Sigma Chemical Co., St. Louis, Mo.) stored at room temperature in a tightly capped bottle; 3',5,5'-tetramethylbenzidine (TMB) (Sigma Chemical Co.) used as a peroxidase substrate and stored at room temperature in the dark to prevent exposure to light; and hydrogen peroxide, 30%.
Several buffers, diluents, and blocking agents are used in the procedure. Note that no sodium azide preservative is used in any of the buffers. This is done to avoid any possible interference from the azide with the peroxidase conjugate.
Phosphate buffered saline (PBS) is prepared by adding 32.0 g sodium chloride, 0.8 g potassium phosphate, monobasic, 0.8 g potassium chloride, and 4.6 g sodium phosphate, dibasic, anhydrous, to 3.2 L deionized water and mixing to dissolve. After bringing the solution to 4 L with deionized water and mixing, the pH is adjusted to about 7.2. The buffer is stored at 4° C. for a maximum of 3 weeks.
The carbonate/bicarbonate coating buffer is prepared by mixing 1.45 g sodium carbonate and 7.25 g sodium bicarbonate in 800 ml deionized water until dissolved. The solution is brought to 1 L with deionized water and mixed, resulting in a pH of approximately 9.2. The buffer is stored at 4° C. for a maximum of 6 weeks.
Two bovine serum albumin solutions (BSA) are utilized as diluents. A 1% BSA solution in PBS, utilized as the second antibody/conjugate diluent, is prepared by adding 1 g BSA (bovine albumin, Fraction V, Sigma Chemical Co.) to 80 ml of PBS, allowing it to stand as it slowly goes into solution, adding PBS to a final volume of 100 ml, and then mixing. This diluent is stored at 4° C. for a maximum of 2 weeks; however if the solution becomes turbid, it is discarded. As a dilent for the standards and samples, a 0.025% BSA solution in PBS is prepared fresh for each assay by diluting the 1% BSA diluent with PBS 1:40 (vol/vol).
A 5% nonfat dry milk (NFDM) blocking agent is prepared fresh for each assay by adding 5 g nonfat dry milk to 100 ml PBS, mixing well to dissolve, and then vacuum filtering through Whatman #3 filter paper. The solution must be filtered to remove particulates prior to use in blocking. A 2.5% NFDM washing buffer is prepared fresh for each assay by diluting the 5% NFDM solution 1:1 (vol/vol) in PBS. Approximately 800 ml is required per assay plate.
The substrate buffer is 0.1M sodium acetate which is brought to a pH of 6.0 with 0.1M citric acid. This buffer is stored at 4° C. for a maximum of 6 weeks.
Immulon I REMOVAWELL strips (Dynatech, Chantilly, Va. #011-010-6301) (polystyrene support comprising 96 wells in an 8 row by 12 column format) are assembled in their holders. Antibody from Example 4 or equivalent is diluted to 25 μg/ml in room temperature coating buffer, and 200 μl is dispensed into each well. The plate is covered and stored overnight at room temperature.
1% BSA, PBS, and substrate buffer are brought to room temperature. 0.025% BSA, 5% NFDM and 2.5% NFDM are prepared fresh for each assay.
Microwells are aspirated with a 12 channel washer. The plate is inverted and blotted on a paper towel to expel residual well contents. 360 μl 5% NFDM is dispensed per well. The plate is covered and placed in a water-bath at 37° C. for 1 hour.
All samples are kept on ice after brief thawing at room temperature. The samples are vortexed, and the required aliquot is removed. Original samples are returned to freezer. If particulate matter is thought to be present, the aliquots of samples are spun in a microfuge and then placed in an ice bath. The samples and standard HCAVIII protein are diluted in 0.025% BSA/PBS. The appropriate dilution series are set up for standard and samples.
The assay plate is removed from the waterbath and each row of the wells is aspirated in turn. Each row of wells is then filled and aspirated in turn with the multiwell washer until the entire plate has been washed once.
Each well is aspirated and then filled with 2.5% NFDM. Each well is then aspirated and the plate blotted forcefully on a paper towel to expel residual well contents. The underside of the plate cover is dried.
Diluted samples and standards are added to the plate at 200 μl/well. The plate is covered and incubated in the 37° C. waterbath for 1 hour.
Rabbit anti-HCAVIII protein is diluted to 500 ng/ml in 1% BSA/PBS at room temperature. The assay plate is removed from the waterbath, samples aspirated and the plate is washed three times. The plate is blotted and 200 μl/well (100 ng/well) of antibody is dispensed. The plate is covered and incubated at 37° C. in the waterbath for 1 hour. Antibody dilution is discarded.
Goat anti-Rabbit IgG/Peroxidase conjugate is diluted to 1:32,000 in 1% BSA/PBS at room temperature. The assay plate is removed from the waterbath, aspirated, and washed three times. The plate is blotted, and the conjugate is dispensed at 200 μl/well. The plate is covered and incubated 1 hour at 37° C. Unused conjugate dilution is discarded.
Substrate mix is prepared 10-15 minutes prior to use by first dissolving TMB at a concentration of 10 mg/ml in DMSO. 29.85 ml substrate buffer is dispensed into a 50 ml centrifuge tube. 150 μl of TMB/DMSO is added and mixed thoroughly. Just prior to use, 50 μl of the substrate mix is discarded and the substrate mix volume is brought back to 30 ml by adding 50 μl 3% H2 O2 (from a 30% stock diluted 1:10 (vol/vol) in substrate buffer). It is mixed thoroughly, and used immediately.
The plate is washed 2 times with 2.5% NFDM and blotted dry. The plate is rewashed 2 times with PBS and blotted dry. 200 μl/well TMB substrate mix is dispensed, the plate covered, and placed in the dark (drawer or covered box). It is incubated 30 minutes at room temperature. A separate well holder is prepared with one REMOVAWELL strip. 200 μl of substrate mix is dispensed into three wells, then 200 μl of deionized water is dispensed into another three wells. These are incubated along with the assay plate.
The peroxidase reaction is stopped by adding 50 μl/well 2M H2 SO4 to all wells. The substrate color will shift from blue to yellow when stopped. If necessary, the well contents may be mixed with the 12 channel dispenser prior to reading the results. Acid can also be added to the six wells containing substrate and deionized water.
The plate is read with a microplate spectrophotometer reader.
Example 6 Carbonic Anhydrase (CA) Activity of Biopsy Tissue
Ice cold solutions of ITB (20 mM imidazole, 5 mM Tris, and 0.4 mMpara-nitrophenol, pH 9.4-9.9) and Buffer A (25 mM triethanolamine, 59 mM H2 SO4, and 1 mM benzamidine HCl) are prepared.
A homogenate is prepared by scraping with a cell scraper into 1-2 ml of Buffer A a monolayer of tissue cells cultured from a tissue sample taken from a biopsy. A portion of the sample is then boiled to inactivate CA.
A tube is placed in an ice water bath. For the macroassay, a 10×75 mm glass tubes and rubber stopper with 16 gauge and 18 gauge needle ports is used; for the microassay, a 6×50 mm glass tube and rubber stopper with 18 gauge needle port and 20 gauge needle with attached PE90 tubing is used. The sample is added along with ice cold water to a final volume of 500 μl for the macroassay or 50 μl for the microassay. 500 μl (macro) or 50 μl (micro) ice cold water is used for a water control. 10 μl antifoam (A. H. Thomas, Philadelphia, Pa.) is added to the tube which is then incubated in ice water for 0.5 to 3 minutes.
The tube is capped with a stopper and CO2 at 150 ml/min (macro) or 100 ml/min (micro) is bubbled through the smaller needle port for 30 sec.
50 μl (macro) or 50 μl (micro) of the ITB solution is rapidly added through the larger needle port with a cold Hamilton syringe. The sample becomes yellow.
Using a timer or stopwatch, the time at which the solution in the tube becomes colorless is measured and recorded. The tube may be momentarily removed from the bath and held in front of a white background to determine the color change. Comparison to a previously acidified sample may be used.
The procedure is repeated with the boiled sample. The volume of sample that corresponds to approximately one enzyme unit is determined using the formula below.
Volume (1EU)=VEU=volume used×log2×log (boiled time/activated time) One enzyme unit is the activity that halves the boiled control time.
The assay is repeated 1-3 times with the sample and boiled sample, using the adjusted volume of sample.
__________________________________________________________________________
SEQUENCE LISTING                                                          
(1) GENERAL INFORMATION:                                                  
(iii) NUMBER OF SEQUENCES: 16                                             
(2) INFORMATION FOR SEQ ID NO:1:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 1104 base pairs                                               
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: both                                                    
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(ix) FEATURE:                                                             
(A) NAME/KEY: CDS                                                         
(B) LOCATION: 32..1093                                                    
(ix) FEATURE:                                                             
(A) NAME/KEY: mat.sub.-- peptide                                          
(B) LOCATION: 119..1093                                                   
(ix) FEATURE:                                                             
(A) NAME/KEY: misc.sub.-- feature                                         
(B) LOCATION: 1013..1024                                                  
(D) OTHER INFORMATION: /note= "phosphorylation site                       
recognized by protein kinase C and other kinases"                         
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:                                   
GCCCGCGCCCGCCCCGCAGGAGCCCGCGAAGATGCCCCGGCGCAGCCTGCAC52                    
MetProArgArgSerLeuHis                                                     
29-25                                                                     
GCGGCGGCCGTGCTCCTGCTGGTGATCTTAAAGGAACAGCCTTCCAGC100                       
AlaAlaAlaValLeuLeuLeuValIleLeuLysGluGlnProSerSer                          
20-15-10                                                                  
CCGGCCCCAGTGAACGGTTCCAAGTGGACTTATTTTGGTCCTGATGGG148                       
ProAlaProValAsnGlySerLysTrpThrTyrPheGlyProAspGly                          
51510                                                                     
GAGAATAGCTGGTCCAAGAAGTACCCGTCGTGTGGGGGCCTGCTGCAG196                       
GluAsnSerTrpSerLysLysTyrProSerCysGlyGlyLeuLeuGln                          
152025                                                                    
TCCCCCATAGACCTGCACAGTGACATCCTCCAGTATGACGCCAGCCTC244                       
SerProIleAspLeuHisSerAspIleLeuGlnTyrAspAlaSerLeu                          
303540                                                                    
ACGCCCCTCGAGTTCCAAGGCTACAATCTGTCTGCCAACAAGCAGTTT292                       
ThrProLeuGluPheGlnGlyTyrAsnLeuSerAlaAsnLysGlnPhe                          
455055                                                                    
CTCCTGACCAACAATGGCCATTCAGTGAAGCTGAACCTGCCCTCGGAC340                       
LeuLeuThrAsnAsnGlyHisSerValLysLeuAsnLeuProSerAsp                          
606570                                                                    
ATGCACATCCAGGGCCTCCAGTCTCGCTACAGTGCCACGCAGCTGCAC388                       
MetHisIleGlnGlyLeuGlnSerArgTyrSerAlaThrGlnLeuHis                          
75808590                                                                  
CTGCACTGGGGGAACCCGAATGACCCGCACGGCTCTGAGCACACCGTC436                       
LeuHisTrpGlyAsnProAsnAspProHisGlySerGluHisThrVal                          
95100105                                                                  
AGCGGACAGCACTTCGCCGCCGAGCTGCACATTGTCCATTATAACTCA484                       
SerGlyGlnHisPheAlaAlaGluLeuHisIleValHisTyrAsnSer                          
110115120                                                                 
GACCTTTATCCTGACGCCAGCACTGCCAGCAACAAGTCAGAAGGCCTC532                       
AspLeuTyrProAspAlaSerThrAlaSerAsnLysSerGluGlyLeu                          
125130135                                                                 
GCTGTCCTGGCTGTTCTCATTGAGATGGGCTCCTTCAATCCGTCCTAT580                       
AlaValLeuAlaValLeuIleGluMetGlySerPheAsnProSerTyr                          
140145150                                                                 
GACAAGATCTTCAGTCACCTTCAACATGTAAAGTACAAAGGCCAGGAA628                       
AspLysIlePheSerHisLeuGlnHisValLysTyrLysGlyGlnGlu                          
155160165170                                                              
GCATTCGTCCCGGGATTCAACATTGAAGAGCTGCTTCCGGAGAGGACC676                       
AlaPheValProGlyPheAsnIleGluGluLeuLeuProGluArgThr                          
175180185                                                                 
GCTGAATATTACCGCTACCGGGGGTCCCTGACCACACCCCCTTGCAAC724                       
AlaGluTyrTyrArgTyrArgGlySerLeuThrThrProProCysAsn                          
190195200                                                                 
CCCACTGTGCTCTGGACAGTTTTCCGAAACCCCGTGCAAATTTCCCAG772                       
ProThrValLeuTrpThrValPheArgAsnProValGlnIleSerGln                          
205210215                                                                 
GAGCAGCTGCTGGCTTTGGAGACAGCCCTGTACTGCACACACATGGAC820                       
GluGlnLeuLeuAlaLeuGluThrAlaLeuTyrCysThrHisMetAsp                          
220225230                                                                 
GACCCTTCCCCCAGAGAAATGATCAACAACTTCCGGCAGGTCCAGAAG868                       
AspProSerProArgGluMetIleAsnAsnPheArgGlnValGlnLys                          
235240245250                                                              
TTCGATGAGAGGCTGGTATACACCTCCTTCTCCCAAGTGCAAGTCTGT916                       
PheAspGluArgLeuValTyrThrSerPheSerGlnValGlnValCys                          
255260265                                                                 
ACTGCGGCAGGACTGAGTCTGGGCATCATCCTCTCACTGGCCCTGGCT964                       
ThrAlaAlaGlyLeuSerLeuGlyIleIleLeuSerLeuAlaLeuAla                          
270275280                                                                 
GGCATTCTTGGCATCTGTATTGTGGTGGTGGTGTCCATTTGGCTTTTC1012                      
GlyIleLeuGlyIleCysIleValValValValSerIleTrpLeuPhe                          
285290295                                                                 
AGAAGGAAGAGTATCAAAAAAGGTGATAACAAGGGAGTCATTTACAAG1060                      
ArgArgLysSerIleLysLysGlyAspAsnLysGlyValIleTyrLys                          
300305310                                                                 
CCAGCCACCAAGATGGAGACTGAGGCCCACGCTTGAGGTCCCCG1104                          
ProAlaThrLysMetGluThrGluAlaHisAla                                         
315320325                                                                 
(2) INFORMATION FOR SEQ ID NO:2:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 354 amino acids                                               
(B) TYPE: amino acid                                                      
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: protein                                               
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:                                   
MetProArgArgSerLeuHisAlaAlaAlaValLeuLeuLeuValIle                          
29- 25-20-15                                                              
LeuLysGluGlnProSerSerProAlaProValAsnGlySerLysTrp                          
10-51                                                                     
ThrTyrPheGlyProAspGlyGluAsnSerTrpSerLysLysTyrPro                          
51015                                                                     
SerCysGlyGlyLeuLeuGlnSerProIleAspLeuHisSerAspIle                          
20253035                                                                  
LeuGlnTyrAspAlaSerLeuThrProLeuGluPheGlnGlyTyrAsn                          
404550                                                                    
LeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGlyHisSerVal                          
556065                                                                    
LysLeuAsnLeuProSerAspMetHisIleGlnGlyLeuGlnSerArg                          
707580                                                                    
TyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnProAsnAspPro                          
859095                                                                    
HisGlySerGluHisThrValSerGlyGlnHisPheAlaAlaGluLeu                          
100105110115                                                              
HisIleValHisTyrAsnSerAspLeuTyrProAspAlaSerThrAla                          
120125130                                                                 
SerAsnLysSerGluGlyLeuAlaValLeuAlaValLeuIleGluMet                          
135140145                                                                 
GlySerPheAsnProSerTyrAspLysIlePheSerHisLeuGlnHis                          
150155160                                                                 
ValLysTyrLysGlyGlnGluAlaPheValProGlyPheAsnIleGlu                          
165170175                                                                 
GluLeuLeuProGluArgThrAlaGluTyrTyrArgTyrArgGlySer                          
180185190195                                                              
LeuThrThrProProCysAsnProThrValLeuTrpThrValPheArg                          
200205210                                                                 
AsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeuGluThrAla                          
215220225                                                                 
LeuTyrCysThrHisMetAspAspProSerProArgGluMetIleAsn                          
230235240                                                                 
AsnPheArgGlnValGlnLysPheAspGluArgLeuValTyrThrSer                          
245250255                                                                 
PheSerGlnValGlnValCysThrAlaAlaGlyLeuSerLeuGlyIle                          
260265270275                                                              
IleLeuSerLeuAlaLeuAlaGlyIleLeuGlyIleCysIleValVal                          
280285290                                                                 
ValValSerIleTrpLeuPheArgArgLysSerIleLysLysGlyAsp                          
295300305                                                                 
AsnLysGlyValIleTyrLysProAlaThrLysMetGluThrGluAla                          
310315320                                                                 
HisAla                                                                    
325                                                                       
(2) INFORMATION FOR SEQ ID NO:3:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 986 base pairs                                                
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: both                                                    
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(ix) FEATURE:                                                             
(A) NAME/KEY: CDS                                                         
(B) LOCATION: 1..975                                                      
(ix) FEATURE:                                                             
(A) NAME/KEY: misc.sub.-- feature                                         
(B) LOCATION: 895..906                                                    
(D) OTHER INFORMATION: /note= "phosphorylation site                       
recognized by protein C kinase and other kinases"                         
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:                                   
TCCAAGTGGACTTATTTTGGTCCTGATGGGGAGAATAGCTGGTCCAAG48                        
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
AAGTACCCGTCGTGTGGGGGCCTGCTGCAGTCCCCCATAGACCTGCAC96                        
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
AGTGACATCCTCCAGTATGACGCCAGCCTCACGCCCCTCGAGTTCCAA144                       
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GGCTACAATCTGTCTGCCAACAAGCAGTTTCTCCTGACCAACAATGGC192                       
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
CATTCAGTGAAGCTGAACCTGCCCTCGGACATGCACATCCAGGGCCTC240                       
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
CAGTCTCGCTACAGTGCCACGCAGCTGCACCTGCACTGGGGGAACCCG288                       
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AATGACCCGCACGGCTCTGAGCACACCGTCAGCGGACAGCACTTCGCC336                       
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
GCCGAGCTGCACATTGTCCATTATAACTCAGACCTTTATCCTGACGCC384                       
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
AGCACTGCCAGCAACAAGTCAGAAGGCCTCGCTGTCCTGGCTGTTCTC432                       
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
ATTGAGATGGGCTCCTTCAATCCGTCCTATGACAAGATCTTCAGTCAC480                       
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
CTTCAACATGTAAAGTACAAAGGCCAGGAAGCATTCGTCCCGGGATTC528                       
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AACATTGAAGAGCTGCTTCCGGAGAGGACCGCTGAATATTACCGCTAC576                       
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
CGGGGGTCCCTGACCACACCCCCTTGCAACCCCACTGTGCTCTGGACA624                       
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
GTTTTCCGAAACCCCGTGCAAATTTCCCAGGAGCAGCTGCTGGCTTTG672                       
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GAGACAGCCCTGTACTGCACACACATGGACGACCCTTCCCCCAGAGAA720                       
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
ATGATCAACAACTTCCGGCAGGTCCAGAAGTTCGATGAGAGGCTGGTA768                       
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TACACCTCCTTCTCCCAAGTGCAAGTCTGTACTGCGGCAGGACTGAGT816                       
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeuSer                          
260265270                                                                 
CTGGGCATCATCCTCTCACTGGCCCTGGCTGGCATTCTTGGCATCTGT864                       
LeuGlyIleIleLeuSerLeuAlaLeuAlaGlyIleLeuGlyIleCys                          
275280285                                                                 
ATTGTGGTGGTGGTGTCCATTTGGCTTTTCAGAAGGAAGAGTATCAAA912                       
IleValValValValSerIleTrpLeuPheArgArgLysSerIleLys                          
290295300                                                                 
AAAGGTGATAACAAGGGAGTCATTTACAAGCCAGCCACCAAGATGGAG960                       
LysGlyAspAsnLysGlyValIleTyrLysProAlaThrLysMetGlu                          
305310315320                                                              
ACTGAGGCCCACGCTTGAGGTCCCCG986                                             
ThrGluAlaHisAla                                                           
325                                                                       
(2) INFORMATION FOR SEQ ID NO:4:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 325 amino acids                                               
(B) TYPE: amino acid                                                      
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: protein                                               
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:                                   
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeuSer                          
260265270                                                                 
LeuGlyIleIleLeuSerLeuAlaLeuAlaGlyIleLeuGlyIleCys                          
275280285                                                                 
IleValValValValSerIleTrpLeuPheArgArgLysSerIleLys                          
290295300                                                                 
LysGlyAspAsnLysGlyValIleTyrLysProAlaThrLysMetGlu                          
305310315320                                                              
ThrGluAlaHisAla                                                           
325                                                                       
(2) INFORMATION FOR SEQ ID NO:5:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 12 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: both                                                    
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(ix) FEATURE:                                                             
(A) NAME/KEY: CDS                                                         
(B) LOCATION: 1..12                                                       
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:                                   
AGAAGGAAGAGT12                                                            
ArgArgLysSer                                                              
(2) INFORMATION FOR SEQ ID NO:6:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 4 amino acids                                                 
(B) TYPE: amino acid                                                      
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: protein                                               
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:                                   
ArgArgLysSer                                                              
1                                                                         
(2) INFORMATION FOR SEQ ID NO:7:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 10 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: DNA                                                   
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:                                   
TGAGTCGACG10                                                              
(2) INFORMATION FOR SEQ ID NO:8:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 14 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: DNA                                                   
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:                                   
AATTCGTCGACTCA14                                                          
(2) INFORMATION FOR SEQ ID NO:9:                                          
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 813 base pairs                                                
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: both                                                    
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(ix) FEATURE:                                                             
(A) NAME/KEY: CDS                                                         
(B) LOCATION: 1..813                                                      
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:                                   
TCCAAGTGGACTTATTTTGGTCCTGATGGGGAGAATAGCTGGTCCAAG48                        
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
AAGTACCCGTCGTGTGGGGGCCTGCTGCAGTCCCCCATAGACCTGCAC96                        
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
AGTGACATCCTCCAGTATGACGCCAGCCTCACGCCCCTCGAGTTCCAA144                       
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GGCTACAATCTGTCTGCCAACAAGCAGTTTCTCCTGACCAACAATGGC192                       
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
CATTCAGTGAAGCTGAACCTGCCCTCGGACATGCACATCCAGGGCCTC240                       
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
CAGTCTCGCTACAGTGCCACGCAGCTGCACCTGCACTGGGGGAACCCG288                       
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AATGACCCGCACGGCTCTGAGCACACCGTCAGCGGACAGCACTTCGCC336                       
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
GCCGAGCTGCACATTGTCCATTATAACTCAGACCTTTATCCTGACGCC384                       
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
AGCACTGCCAGCAACAAGTCAGAAGGCCTCGCTGTCCTGGCTGTTCTC432                       
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
ATTGAGATGGGCTCCTTCAATCCGTCCTATGACAAGATCTTCAGTCAC480                       
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
CTTCAACATGTAAAGTACAAAGGCCAGGAAGCATTCGTCCCGGGATTC528                       
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AACATTGAAGAGCTGCTTCCGGAGAGGACCGCTGAATATTACCGCTAC576                       
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
CGGGGGTCCCTGACCACACCCCCTTGCAACCCCACTGTGCTCTGGACA624                       
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
GTTTTCCGAAACCCCGTGCAAATTTCCCAGGAGCAGCTGCTGGCTTTG672                       
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GAGACAGCCCTGTACTGCACACACATGGACGACCCTTCCCCCAGAGAA720                       
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
ATGATCAACAACTTCCGGCAGGTCCAGAAGTTCGATGAGAGGCTGGTA768                       
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TACACCTCCTTCTCCCAAGTGCAAGTCTGTACTGCGGCAGGACTG813                          
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeu                             
260265270                                                                 
(2) INFORMATION FOR SEQ ID NO:10:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 271 amino acids                                               
(B) TYPE: amino acid                                                      
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: protein                                               
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:                                  
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeu                             
260265270                                                                 
(2) INFORMATION FOR SEQ ID NO:11:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 25 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:                                  
CTTTTTTGATACCCTTCCTTCTGAA25                                               
(2) INFORMATION FOR SEQ ID NO:12:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 986 base pairs                                                
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: both                                                    
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(ix) FEATURE:                                                             
(A) NAME/KEY: CDS                                                         
(B) LOCATION: 1..975                                                      
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:                                  
TCCAAGTGGACTTATTTTGGTCCTGATGGGGAGAATAGCTGGTCCAAG48                        
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
AAGTACCCGTCGTGTGGGGGCCTGCTGCAGTCCCCCATAGACCTGCAC96                        
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
AGTGACATCCTCCAGTATGACGCCAGCCTCACGCCCCTCGAGTTCCAA144                       
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GGCTACAATCTGTCTGCCAACAAGCAGTTTCTCCTGACCAACAATGGC192                       
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
CATTCAGTGAAGCTGAACCTGCCCTCGGACATGCACATCCAGGGCCTC240                       
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
CAGTCTCGCTACAGTGCCACGCAGCTGCACCTGCACTGGGGGAACCCG288                       
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AATGACCCGCACGGCTCTGAGCACACCGTCAGCGGACAGCACTTCGCC336                       
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
GCCGAGCTGCACATTGTCCATTATAACTCAGACCTTTATCCTGACGCC384                       
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
AGCACTGCCAGCAACAAGTCAGAAGGCCTCGCTGTCCTGGCTGTTCTC432                       
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
ATTGAGATGGGCTCCTTCAATCCGTCCTATGACAAGATCTTCAGTCAC480                       
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
CTTCAACATGTAAAGTACAAAGGCCAGGAAGCATTCGTCCCGGGATTC528                       
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AACATTGAAGAGCTGCTTCCGGAGAGGACCGCTGAATATTACCGCTAC576                       
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
CGGGGGTCCCTGACCACACCCCCTTGCAACCCCACTGTGCTCTGGACA624                       
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
GTTTTCCGAAACCCCGTGCAAATTTCCCAGGAGCAGCTGCTGGCTTTG672                       
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GAGACAGCCCTGTACTGCACACACATGGACGACCCTTCCCCCAGAGAA720                       
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
ATGATCAACAACTTCCGGCAGGTCCAGAAGTTCGATGAGAGGCTGGTA768                       
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TACACCTCCTTCTCCCAAGTGCAAGTCTGTACTGCGGCAGGACTGAGT816                       
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeuSer                          
260265270                                                                 
CTGGGCATCATCCTCTCACTGGCCCTGGCTGGCATTCTTGGCATCTGT864                       
LeuGlyIleIleLeuSerLeuAlaLeuAlaGlyIleLeuGlyIleCys                          
275280285                                                                 
ATTGTGGTGGTGGTGTCCATTTGGCTTTTCAGAAGGAAGGGTATCAAA912                       
IleValValValValSerIleTrpLeuPheArgArgLysGlyIleLys                          
290295300                                                                 
AAAGGTGATAACAAGGGAGTCATTTACAAGCCAGCCACCAAGATGGAG960                       
LysGlyAspAsnLysGlyValIleTyrLysProAlaThrLysMetGlu                          
305310315320                                                              
ACTGAGGCCCACGCTTGAGGTCCCCG986                                             
ThrGluAlaHisAla                                                           
325                                                                       
(2) INFORMATION FOR SEQ ID NO:13:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 325 amino acids                                               
(B) TYPE: amino acid                                                      
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: protein                                               
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:                                  
SerLysTrpThrTyrPheGlyProAspGlyGluAsnSerTrpSerLys                          
151015                                                                    
LysTyrProSerCysGlyGlyLeuLeuGlnSerProIleAspLeuHis                          
202530                                                                    
SerAspIleLeuGlnTyrAspAlaSerLeuThrProLeuGluPheGln                          
354045                                                                    
GlyTyrAsnLeuSerAlaAsnLysGlnPheLeuLeuThrAsnAsnGly                          
505560                                                                    
HisSerValLysLeuAsnLeuProSerAspMetHisIleGlnGlyLeu                          
65707580                                                                  
GlnSerArgTyrSerAlaThrGlnLeuHisLeuHisTrpGlyAsnPro                          
859095                                                                    
AsnAspProHisGlySerGluHisThrValSerGlyGlnHisPheAla                          
100105110                                                                 
AlaGluLeuHisIleValHisTyrAsnSerAspLeuTyrProAspAla                          
115120125                                                                 
SerThrAlaSerAsnLysSerGluGlyLeuAlaValLeuAlaValLeu                          
130135140                                                                 
IleGluMetGlySerPheAsnProSerTyrAspLysIlePheSerHis                          
145150155160                                                              
LeuGlnHisValLysTyrLysGlyGlnGluAlaPheValProGlyPhe                          
165170175                                                                 
AsnIleGluGluLeuLeuProGluArgThrAlaGluTyrTyrArgTyr                          
180185190                                                                 
ArgGlySerLeuThrThrProProCysAsnProThrValLeuTrpThr                          
195200205                                                                 
ValPheArgAsnProValGlnIleSerGlnGluGlnLeuLeuAlaLeu                          
210215220                                                                 
GluThrAlaLeuTyrCysThrHisMetAspAspProSerProArgGlu                          
225230235240                                                              
MetIleAsnAsnPheArgGlnValGlnLysPheAspGluArgLeuVal                          
245250255                                                                 
TyrThrSerPheSerGlnValGlnValCysThrAlaAlaGlyLeuSer                          
260265270                                                                 
LeuGlyIleIleLeuSerLeuAlaLeuAlaGlyIleLeuGlyIleCys                          
275280285                                                                 
IleValValValValSerIleTrpLeuPheArgArgLysGlyIleLys                          
290295300                                                                 
LysGlyAspAsnLysGlyValIleTyrLysProAlaThrLysMetGlu                          
305310315320                                                              
ThrGluAlaHisAla                                                           
325                                                                       
(2) INFORMATION FOR SEQ ID NO:14:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 21 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:                                  
ACATTGAAGAGCTGCTTCCGG21                                                   
(2) INFORMATION FOR SEQ ID NO:15:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 19 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:                                  
AATTTGCACGGGGTTTCGG19                                                     
(2) INFORMATION FOR SEQ ID NO:16:                                         
(i) SEQUENCE CHARACTERISTICS:                                             
(A) LENGTH: 23 base pairs                                                 
(B) TYPE: nucleic acid                                                    
(C) STRANDEDNESS: single                                                  
(D) TOPOLOGY: linear                                                      
(ii) MOLECULE TYPE: cDNA                                                  
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:                                  
GTCCACTTGGATCCGTTCACTGG23                                                 
__________________________________________________________________________

Claims (15)

We claim:
1. An isolated nucleic acid comprising a nucleotide sequence encoding the amino acid sequence depicted in SEQ ID NO:2.
2. The nucleic acid according to claim 1 wherein said an isolated nucleic acid is mRNA.
3. An isolated cDNA encoding the protein of SEQ ID NO:2.
4. The isolated cDNA of claim 3, comprising the coding sequence of SEQ ID NO:1.
5. An isolated cDNA encoding the protein of SEQ ID NO:4.
6. The isolated cDNA of claim 5, comprising the coding sequence of SEQ ID NO:3.
7. An isolated cDNA encoding the protein of SEQ ID NO:10.
8. The isolated cDNA of claim 7, comprising the coding sequence of SEQ ID NO:9.
9. An isolated cDNA comprising a nucleotide sequence encoding the amino acid sequence depicted in SEQ ID NO:4 except amino acid residue 30 is a single amino acid residue other than Ser.
10. The isolated cDNA of claim 9, comprising the coding sequence of SEQ ID NO:12.
11. An isolated cDNA encoding human carbonic anhydrase VIII of a 1.1 kilobase transcript isolated from human A549 cells.
12. An expression vector comprising the coding region of the sequence depicted in SEQ ID NO: 1.
13. An expression vector comprising the coding region of the sequence depicted in SEQ ID NO:3.
14. An expression vector comprising the coding region the sequence depicted in SEQ ID NO:9.
15. An expression vector comprising the coding region of the sequence depicted in SEQ ID NO: 12.
US08/276,919 1994-07-19 1994-07-19 Gene sequence and probe for a marker of non-small cell lung carinoma Expired - Fee Related US5589579A (en)

Priority Applications (9)

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US08/276,919 US5589579A (en) 1994-07-19 1994-07-19 Gene sequence and probe for a marker of non-small cell lung carinoma
JP8505257A JPH10503087A (en) 1994-07-19 1995-07-19 Lung cancer marker
PCT/US1995/009145 WO1996002552A1 (en) 1994-07-19 1995-07-19 Lung cancer marker
US08/776,088 US5773579A (en) 1994-07-19 1995-07-19 Lung cancer marker
CA002195403A CA2195403A1 (en) 1994-07-19 1995-07-19 Lung cancer marker
AU33592/95A AU700915B2 (en) 1994-07-19 1995-07-19 Lung cancer marker
EP95930093A EP0804451A4 (en) 1994-07-19 1995-07-19 Lung cancer marker
BR9508417A BR9508417A (en) 1994-07-19 1995-07-19 Nucleic acid isolated cdna isolated protein isolated expression vector process to detect cancer and pre-lung cancer process to select human specimens for hcaviii protein process to test human cell sample antibody and therapeutic composition
MXPA/A/1997/000502A MXPA97000502A (en) 1994-07-19 1997-01-17 Pul cancer marker

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US08/276,919 US5589579A (en) 1994-07-19 1994-07-19 Gene sequence and probe for a marker of non-small cell lung carinoma

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US08/776,088 Expired - Fee Related US5773579A (en) 1994-07-19 1995-07-19 Lung cancer marker

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JP (1) JPH10503087A (en)
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BR (1) BR9508417A (en)
CA (1) CA2195403A1 (en)
WO (1) WO1996002552A1 (en)

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